diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index 60c25a5a69820b72a7e5bbd0f17cc8b5f0dac3fe..fb99be4a4f8716c8f96fb6be12d9caa264b249be 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -24,6 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.mutable
import scala.io.Source
+import scala.util.matching.Regex
/**
* Extension for cutadapt
@@ -163,6 +164,51 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
(if (outputAsStsout) "" else required("--output", fastqOutput) +
" > " + required(statsOutput))
+ def extractClippedAdapters(statsOutput: File): Map[String, Any] = {
+ val histoCountRow: Regex = """([\d]+)\t([\d]+)\t.*""".r
+ val adapterR = """Sequence: ([C|T|A|G]+);.*Trimmed: ([\d]+) times\.""".r
+
+ val statsFile = Source.fromFile(statsOutput)
+ val adapterRawStats: Array[String] = statsFile.mkString
+ .split("=== Adapter [\\d]+ ===")
+ .filter(_.contains("Sequence")
+ )
+ statsFile.close()
+
+ adapterRawStats.map(adapter => {
+ var adapterName = ""
+ var adapterCount = 0
+ // identify the adapter name and count
+ for (line <- adapter.split("\n")) {
+ line match {
+ case adapterR(adapter, count) => {
+ adapterName = adapter
+ adapterCount = count.toInt
+ }
+ case _ =>
+ }
+ }
+
+ // parse the block that gives the histogram of clipped bases and from which end
+ val counts = adapter.split("Overview of removed sequences ")
+ .filter(x => x.contains("length"))
+ .map(clipSideRawStats => {
+ val clipSideLabel = if (clipSideRawStats.contains("5'")) { "5p" } else { "3p" }
+
+ val histogramValues = clipSideRawStats.split("\n").flatMap({
+ case histoCountRow(length, count) => Some(length.toInt -> count.toInt)
+ case _ => None
+ })
+ clipSideLabel -> histogramValues.toMap
+ })
+
+ adapterName -> Map(
+ "count" -> adapterCount,
+ "histogram" -> counts.toMap
+ )
+ }).toMap // converting the Array[String] containing map-items to Map with 'toMap'
+ }
+
/** Output summary stats */
def summaryStats: Map[String, Any] = {
/**
@@ -177,7 +223,6 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
val tooLongR = """.* that were too long: *([,\d]+) .*""".r
val tooManyN = """.* with too many N: *([,\d]+) .*""".r
- val adapterR = """Sequence ([C|T|A|G]*);.*Trimmed: ([,\d]+) times.""".r
val basePairsProcessed = """Total basepairs processed: *([,\d]+) bp""".r
val basePairsWritten = """Total written \(filtered\): *([,\d]+) bp .*""".r
@@ -192,24 +237,28 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
"bpoutput" -> 0,
"toomanyn" -> 0
)
- val adapterStats: mutable.Map[String, Long] = mutable.Map()
+
+ // extract the adapters with its histogram
+ val adapterStats = if (statsOutput.exists) {
+ extractClippedAdapters(statsOutput)
+ } else Map.empty
if (statsOutput.exists) {
val statsFile = Source.fromFile(statsOutput)
for (line <- statsFile.getLines()) {
line match {
- case processedReads(m) => stats("processed") = m.replaceAll(",", "").toLong
- case withAdapters(m) => stats("withadapters") = m.replaceAll(",", "").toLong
- case readsPassingFilters(m) => stats("passingfilters") = m.replaceAll(",", "").toLong
- case tooShortR(m) => stats("tooshort") = m.replaceAll(",", "").toLong
- case tooLongR(m) => stats("toolong") = m.replaceAll(",", "").toLong
- case tooManyN(m) => stats("toomanyn") = m.replaceAll(",", "").toLong
- case basePairsProcessed(m) => stats("bpinput") = m.replaceAll(",", "").toLong
- case basePairsWritten(m) => stats("bpoutput") = m.replaceAll(",", "").toLong
- case adapterR(adapter, count) => adapterStats += (adapter -> count.toLong)
- case _ =>
+ case processedReads(m) => stats("processed") = m.replaceAll(",", "").toLong
+ case withAdapters(m) => stats("withadapters") = m.replaceAll(",", "").toLong
+ case readsPassingFilters(m) => stats("passingfilters") = m.replaceAll(",", "").toLong
+ case tooShortR(m) => stats("tooshort") = m.replaceAll(",", "").toLong
+ case tooLongR(m) => stats("toolong") = m.replaceAll(",", "").toLong
+ case tooManyN(m) => stats("toomanyn") = m.replaceAll(",", "").toLong
+ case basePairsProcessed(m) => stats("bpinput") = m.replaceAll(",", "").toLong
+ case basePairsWritten(m) => stats("bpoutput") = m.replaceAll(",", "").toLong
+ case _ =>
}
}
+ statsFile.close()
}
val cleanReads = stats("processed") - stats("withadapters")
@@ -223,8 +272,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
"num_reads_discarded_too_long" -> stats("toolong"),
"num_reads_discarded_many_n" -> stats("toomanyn"),
"num_bases_input" -> stats("bpinput"),
- "num_based_output" -> stats("bpoutput"),
- adaptersStatsName -> adapterStats.toMap
+ "num_bases_output" -> stats("bpoutput"),
+ adaptersStatsName -> adapterStats
)
}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index fc8db7ab30f7581c7638f15c48bba6e9443eb195..3cb06df0e160cb97b98710de74f7ca9fa31ce919 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.utils.config.Configurable
+import scala.collection.JavaConversions._
/**
* Cutadapt wrapper specific for Flexiprep.
@@ -41,23 +42,26 @@ class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.e
val adapterCounts: Map[String, Any] = initStats.get(adaptersStatsName) match {
// "adapters" key found in statistics
case Some(m: Map[_, _]) => m.flatMap {
- case (seq: String, count) =>
- seqToNameMap.get(seq) match {
+ case (adapterSequence: String, adapterStats: Map[_, _]) =>
+ seqToNameMap.get(adapterSequence) match {
// adapter sequence is found by FastQC
- case Some(n) => Some(n -> Map("sequence" -> seq, "count" -> count))
+ case Some(adapterSeqName) => {
+ Some(adapterSeqName ->
+ Map("sequence" -> adapterSequence, "stats" -> adapterStats.toMap)
+ )
+ }
// adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
// sequences come from FastQC
case _ =>
- throw new IllegalStateException(s"Adapter '$seq' is clipped but not found by FastQC in '$fastqInput'.")
+ throw new IllegalStateException(s"Adapter '$adapterSequence' is clipped but not found by FastQC in '$fastqInput'.")
}
// FastQC found no adapters
case otherwise =>
- ;
logger.debug(s"No adapters found for summarizing in '$fastqInput'.")
None
}
// "adapters" key not found ~ something went wrong in our part
- case _ => throw new RuntimeException(s"Required key 'adapters' not found in stats entry '$fastqInput'.")
+ case _ => throw new RuntimeException(s"Required key '${adaptersStatsName}' not found in stats entry '${fastqInput}'.")
}
initStats.updated(adaptersStatsName, adapterCounts)
}
diff --git a/flexiprep/src/test/resources/ct-test.R1.clip.stats b/flexiprep/src/test/resources/ct-test.R1.clip.stats
new file mode 100644
index 0000000000000000000000000000000000000000..4a280ef0a7d2588169c02b5e40432f4f903c69b8
--- /dev/null
+++ b/flexiprep/src/test/resources/ct-test.R1.clip.stats
@@ -0,0 +1,160 @@
+This is cutadapt 1.9.1 with Python 2.7.6
+Command line parameters: -b CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG -b CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG --error-rate 0.2 --times 2 -m 15 ct_r1.fq.gz.seqtk.fq --output ct_r1.fq.gz.cutadapt.fq
+Trimming 4 adapters with at most 20.0% errors in single-end mode ...
+Finished in 0.19 s (189 us/read; 0.32 M reads/minute).
+
+=== Summary ===
+
+Total reads processed: 1,000
+Reads with adapters: 440 (44.0%)
+Reads that were too short: 15 (1.5%)
+Reads written (passing filters): 985 (98.5%)
+
+Total basepairs processed: 100,000 bp
+Total written (filtered): 89,423 bp (89.4%)
+
+=== Adapter 1 ===
+
+Sequence: CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC; Type: variable 5'/3'; Length: 63; Trimmed: 94 times.
+18 times, it overlapped the 5' end of a read
+76 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length count expect max.err error counts
+3 8 15.6 0 8
+4 3 3.9 0 2 1
+5 2 1.0 1 0 2
+6 4 0.2 1 1 3
+9 1 0.0 1 0 0 1
+
+
+Overview of removed sequences (3' or within)
+length count expect max.err error counts
+3 13 15.6 0 13
+4 19 3.9 0 3 16
+5 21 1.0 1 0 21
+6 18 0.2 1 1 17
+7 2 0.1 1 0 2
+9 1 0.0 1 0 0 1
+11 1 0.0 2 0 0 1
+12 1 0.0 2 0 0 1
+
+=== Adapter 2 ===
+
+Sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG; Type: variable 5'/3'; Length: 63; Trimmed: 340 times.
+117 times, it overlapped the 5' end of a read
+223 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length count expect max.err error counts
+3 14 15.6 0 14
+4 29 3.9 0 6 23
+5 32 1.0 1 3 29
+6 36 0.2 1 0 36
+8 1 0.0 1 0 1
+9 1 0.0 1 0 0 1
+10 1 0.0 2 0 0 1
+11 2 0.0 2 0 0 2
+37 1 0.0 7 0 0 0 0 0 1
+
+
+Overview of removed sequences (3' or within)
+length count expect max.err error counts
+3 18 15.6 0 18
+4 9 3.9 0 5 4
+5 15 1.0 1 8 7
+6 10 0.2 1 8 2
+7 7 0.1 1 5 2
+8 10 0.0 1 9 1
+9 6 0.0 1 5 1
+10 8 0.0 2 5 0 3
+11 4 0.0 2 4
+12 4 0.0 2 4
+13 9 0.0 2 9
+14 4 0.0 2 3 0 1
+15 7 0.0 3 7
+16 2 0.0 3 2
+17 4 0.0 3 2 1 0 1
+18 2 0.0 3 2
+19 2 0.0 3 2
+20 2 0.0 4 0 1 1
+21 7 0.0 4 6 1
+22 7 0.0 4 7
+23 2 0.0 4 2
+24 3 0.0 4 3
+25 5 0.0 5 5
+26 5 0.0 5 5
+27 8 0.0 5 8
+28 6 0.0 5 5 1
+29 2 0.0 5 2
+30 5 0.0 6 5
+31 3 0.0 6 3
+32 8 0.0 6 8
+33 1 0.0 6 1
+34 5 0.0 6 0 5
+35 2 0.0 7 0 0 0 0 0 0 2
+36 3 0.0 7 0 0 0 0 0 0 3
+37 4 0.0 7 0 0 0 0 0 0 0 2 2
+38 2 0.0 7 0 0 0 0 0 0 0 0 0 2
+39 4 0.0 7 0 0 0 0 1 0 0 0 0 3
+40 3 0.0 8 0 0 0 0 0 0 0 3
+41 1 0.0 8 0 0 0 0 0 0 0 1
+42 4 0.0 8 0 0 0 0 0 0 0 0 4
+43 5 0.0 8 0 0 0 0 0 0 0 0 0 5
+44 3 0.0 8 0 0 0 0 0 0 0 0 0 0 3
+46 1 0.0 9 0 0 0 0 0 0 0 0 0 0 1
+49 1 0.0 9 0 0 0 0 0 1
+
+=== Adapter 3 ===
+
+Sequence: CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC; Type: variable 5'/3'; Length: 63; Trimmed: 0 times.
+
+=== Adapter 4 ===
+
+Sequence: GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG; Type: variable 5'/3'; Length: 63; Trimmed: 82 times.
+15 times, it overlapped the 5' end of a read
+67 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3; 20-24 bp: 4; 25-29 bp: 5; 30-34 bp: 6; 35-39 bp: 7; 40-44 bp: 8; 45-49 bp: 9; 50-54 bp: 10; 55-59 bp: 11; 60-63 bp: 12
+
+Overview of removed sequences (5')
+length count expect max.err error counts
+26 1 0.0 5 0 1
+61 2 0.0 12 0 0 0 2
+64 11 0.0 12 0 0 0 11
+72 1 0.0 12 0 0 0 0 0 0 0 0 0 0 0 1
+
+
+Overview of removed sequences (3' or within)
+length count expect max.err error counts
+45 3 0.0 9 0 0 0 3
+46 2 0.0 9 0 0 0 2
+47 3 0.0 9 0 0 0 3
+48 3 0.0 9 0 0 0 3
+49 2 0.0 9 0 0 0 2
+50 3 0.0 10 0 0 0 3
+51 2 0.0 10 0 0 0 2
+52 6 0.0 10 0 0 0 6
+53 1 0.0 10 0 0 0 1
+54 5 0.0 10 0 0 0 4 0 1
+56 2 0.0 11 0 0 0 2
+57 2 0.0 11 0 0 0 2
+58 2 0.0 11 0 0 0 2
+59 3 0.0 11 0 0 0 2 0 0 0 0 0 1
+61 1 0.0 12 0 0 0 0 0 1
+62 3 0.0 12 0 0 0 2 1
+63 1 0.0 12 0 0 0 0 1
+66 3 0.0 12 0 0 0 3
+67 3 0.0 12 0 0 0 3
+70 1 0.0 12 0 0 0 1
+72 1 0.0 12 0 0 0 1
+80 1 0.0 12 0 0 0 1
+99 14 0.0 12 0 0 0 14
+
diff --git a/flexiprep/src/test/resources/fqc_contaminants_v0112.txt b/flexiprep/src/test/resources/fqc_contaminants_v0112.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2c29bee8171e0454994c6d7d6f0f4780efb3921
--- /dev/null
+++ b/flexiprep/src/test/resources/fqc_contaminants_v0112.txt
@@ -0,0 +1,182 @@
+# This file contains a list of potential contaminants which are
+# frequently found in high throughput sequencing reactions. These
+# are mostly sequences of adapters / primers used in the various
+# sequencing chemistries.
+#
+# Please DO NOT rely on these sequences to design your own oligos, some
+# of them are truncated at ambiguous positions, and none of them are
+# definitive sequences from the manufacturers so don't blame us if you
+# try to use them and they don't work.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence. If the contaminant you add is
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.babraham.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@babraham.ac.uk so other users of
+# the program can benefit.
+
+Illumina Single End Adapter 1 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
+Illumina Single End Adapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+Illumina Paired End Adapter 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Adapter 2 GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
+Illumina Paried End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End PCR Primer 2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End Sequencing Primer 1 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Sequencing Primer 2 CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+
+Illumina DpnII expression Adapter 1 ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII expression Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII expression Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII expression Adapter 1 ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII expression Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII expression Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA Adapter 1 GTTCAGAGTTCTACAGTCCGACGATC
+Illumina Small RNA Adapter 2 TGGAATTCTCGGGTGCCAAGG
+Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina Multiplexing Adapter 1 GATCGGAAGAGCACACGTCT
+Illumina Multiplexing Adapter 2 ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 1.01 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 2.01 GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+Illumina Multiplexing Read1 Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing Index Sequencing Primer GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+Illumina Multiplexing Read2 Sequencing Primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
+Illumina PCR Primer Index 1 CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
+Illumina PCR Primer Index 2 CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
+Illumina PCR Primer Index 3 CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
+Illumina PCR Primer Index 4 CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
+Illumina PCR Primer Index 5 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
+Illumina PCR Primer Index 6 CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
+Illumina PCR Primer Index 7 CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
+Illumina PCR Primer Index 8 CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
+Illumina PCR Primer Index 9 CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
+Illumina PCR Primer Index 10 CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
+Illumina PCR Primer Index 11 CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
+Illumina PCR Primer Index 12 CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
+
+Illumina DpnII Gex Adapter 1 GATCGTCGGACTGTAGAACTCTGAAC
+Illumina DpnII Gex Adapter 1.01 ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII Gex Adapter 2 CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex Adapter 2.01 TCGTATGCCGTCTTCTGCTTG
+Illumina DpnII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII Gex Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII Gex Adapter 1.01 TCGGACTGTAGAACTCTGAAC
+Illumina NlaIII Gex Adapter 1.02 ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII Gex Adapter 2.01 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex Adapter 2.02 TCGTATGCCGTCTTCTGCTTG
+Illumina NlaIII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII Gex Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
+Illumina 5p RNA Adapter GTTCAGAGTTCTACAGTCCGACGATC
+Illumina RNA Adapter1 TGGAATTCTCGGGTGCCAAGG
+
+Illumina Small RNA 3p Adapter 1 ATCTCGTATGCCGTCTTCTGCTTG
+Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
+Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+TruSeq Universal Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+TruSeq Adapter, Index 1 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 2 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 3 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 4 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 6 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 7 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 8 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 9 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 10 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 11 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 12 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 13 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 14 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 15 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 16 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 18 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 19 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 20 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 21 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 22 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 23 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCACTCTTCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 25 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 27 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTCTCGTATGCCGTCTTCTGCTTG
+
+Illumina RNA RT Primer GCCTTGGCACCCGAGAATTCCA
+Illumina RNA PCR Primer AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
+
+RNA PCR Primer, Index 1 CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 2 CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 3 CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 4 CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 5 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 6 CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 7 CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 8 CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 9 CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 10 CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 11 CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 12 CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 13 CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 14 CAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 15 CAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 16 CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 17 CAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 18 CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 19 CAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 20 CAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 21 CAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 22 CAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 23 CAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 24 CAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 25 CAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 26 CAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 27 CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 28 CAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 29 CAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 30 CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 31 CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 32 CAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 33 CAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 34 CAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 35 CAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 36 CAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 37 CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 38 CAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 39 CAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 40 CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 41 CAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 42 CAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 43 CAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 44 CAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 45 CAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 46 CAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 47 CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 48 CAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+
+ABI Dynabead EcoP Oligo CTGATCTAGAGGTACCGGATCCCAGCAGT
+ABI Solid3 Adapter A CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
+ABI Solid3 Adapter B CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
+ABI Solid3 5' AMP Primer CCACTACGCCTCCGCTTTCCTCTCTATG
+ABI Solid3 3' AMP Primer CTGCCCCGGGTTCCTCATTCT
+ABI Solid3 EF1 alpha Sense Primer CATGTGTGTTGAGAGCTTC
+ABI Solid3 EF1 alpha Antisense Primer GAAAACCAAAGTGGTCCAC
+ABI Solid3 GAPDH Forward Primer TTAGCACCCCTGGCCAAGG
+ABI Solid3 GAPDH Reverse Primer CTTACTCCTTGGAGGCCATG
diff --git a/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt b/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
index 74938a52b7d505b1185b1962ffe7234ddb304a52..02b9e3f0cbf01c6ce54fa715df93d7cfc6ba4bab 100644
--- a/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
+++ b/flexiprep/src/test/resources/v0101.fq_fastqc/fastqc_data.txt
@@ -1,29 +1,13 @@
-====
- Biopet is built on top of GATK Queue for building bioinformatic
- pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- should also be able to execute Biopet tools and pipelines.
-
- Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-
- Contact us at: sasc@lumc.nl
-
- A dual licensing mode is applied. The source code within this project that are
- not part of GATK Queue is freely available for non-commercial use under an AGPL
- license; For commercial users or users who do not want to follow the AGPL
- license, please contact us to obtain a separate license.
-====
-
-##FastQC 0.10.1
+##FastQC 0.11.2
>>Basic Statistics pass
-#Measure Value
-Filename ct_r1.fq
-File type Conventional base calls
-Encoding Sanger / Illumina 1.9
-Total Sequences 1000
-Filtered Sequences 0
-Sequence length 100
-%GC 53
+#Measure Value
+Filename ct_r1.fq.gz
+File type Conventional base calls
+Encoding Sanger / Illumina 1.9
+Total Sequences 1000
+Sequences flagged as poor quality 0
+Sequence length 100
+%GC 53
>>END_MODULE
>>Per base sequence quality fail
#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
@@ -36,26 +20,111 @@ Sequence length 100
7 35.783 37.0 35.0 37.0 35.0 37.0
8 36.008 37.0 35.0 37.0 35.0 37.0
9 37.706 39.0 37.0 39.0 35.0 39.0
-10-14 37.857600000000005 39.2 37.2 39.4 34.8 39.4
-15-19 38.9788 40.2 38.0 41.0 35.0 41.0
-20-24 38.8246 40.0 38.0 41.0 34.8 41.0
-25-29 38.589600000000004 40.0 38.0 41.0 34.4 41.0
-30-34 38.3568 40.0 38.0 41.0 33.8 41.0
-35-39 38.1592 40.0 37.4 41.0 33.6 41.0
-40-44 37.4808 39.8 36.0 41.0 32.6 41.0
-45-49 36.9478 39.0 35.0 40.8 31.2 41.0
-50-54 35.845600000000005 37.8 34.6 40.0 29.4 41.0
-55-59 34.739 36.6 33.6 40.0 27.4 41.0
-60-64 34.1336 35.4 33.4 38.6 27.2 40.2
-65-69 32.7464 35.0 32.6 37.2 24.6 39.6
-70-74 29.3478 34.0 29.6 35.6 2.0 38.6
-75-79 27.4908 33.2 26.4 35.0 2.0 36.6
-80-84 25.893000000000008 33.0 21.8 35.0 2.0 35.4
-85-89 25.031799999999997 32.4 16.2 34.6 2.0 35.0
-90-94 23.9446 31.4 6.4 34.0 2.0 35.0
-95-99 22.9358 30.4 2.0 34.0 2.0 35.0
+10-11 37.709 39.0 37.0 39.0 35.0 39.0
+12-13 37.6135 39.0 37.0 39.0 35.0 39.0
+14-15 38.793 40.0 38.0 41.0 34.5 41.0
+16-17 39.033500000000004 40.5 38.0 41.0 35.0 41.0
+18-19 38.942 40.0 38.0 41.0 35.0 41.0
+20-21 38.888 40.0 38.0 41.0 35.0 41.0
+22-23 38.807 40.0 38.0 41.0 35.0 41.0
+24-25 38.702 40.0 38.0 41.0 34.0 41.0
+26-27 38.65 40.0 38.0 41.0 34.5 41.0
+28-29 38.4885 40.0 38.0 41.0 34.5 41.0
+30-31 38.307 40.0 38.0 41.0 34.0 41.0
+32-33 38.433499999999995 40.0 38.0 41.0 34.0 41.0
+34-35 38.3425 40.0 38.0 41.0 33.5 41.0
+36-37 38.1185 40.0 37.5 41.0 33.5 41.0
+38-39 38.088499999999996 40.0 37.0 41.0 33.5 41.0
+40-41 37.555 40.0 36.0 41.0 32.5 41.0
+42-43 37.504999999999995 40.0 36.0 41.0 33.0 41.0
+44-45 37.167 39.0 35.5 41.0 32.0 41.0
+46-47 36.980999999999995 39.0 35.0 41.0 31.0 41.0
+48-49 36.8635 39.0 35.0 40.5 31.0 41.0
+50-51 36.4125 38.5 35.0 40.0 30.5 41.0
+52-53 35.528000000000006 37.5 34.5 40.0 28.5 41.0
+54-55 34.925 37.0 33.5 40.0 27.5 41.0
+56-57 34.8735 37.0 34.0 40.0 27.5 41.0
+58-59 34.7225 36.0 33.5 40.0 28.0 41.0
+60-61 34.67400000000001 36.0 34.0 39.0 28.5 40.5
+62-63 33.841499999999996 35.0 33.0 38.5 26.5 40.0
+64-65 33.549 35.0 33.0 38.0 26.0 40.0
+66-67 32.971999999999994 35.0 33.0 37.0 26.0 40.0
+68-69 32.1635 35.0 32.0 37.0 22.5 39.0
+70-71 30.002000000000002 34.0 30.5 36.0 2.0 39.0
+72-73 29.0695 34.0 29.0 35.5 2.0 38.5
+74-75 28.641 34.0 29.0 35.0 2.0 38.0
+76-77 27.8495 33.0 27.5 35.0 2.0 36.0
+78-79 26.5345 33.0 24.0 35.0 2.0 36.5
+80-81 26.140500000000003 33.0 23.0 35.0 2.0 36.0
+82-83 25.784 33.0 21.5 35.0 2.0 35.0
+84-85 25.6115 33.0 20.0 35.0 2.0 35.0
+86-87 25.1755 33.0 17.0 35.0 2.0 35.0
+88-89 24.600499999999997 31.5 13.5 34.0 2.0 35.0
+90-91 24.088 31.5 6.5 34.0 2.0 35.0
+92-93 24.16 32.0 8.5 34.0 2.0 35.0
+94-95 23.02 30.0 2.0 34.0 2.0 35.0
+96-97 23.183 30.5 2.0 34.0 2.0 35.0
+98-99 22.75 30.5 2.0 34.0 2.0 35.0
100 21.984 30.0 2.0 34.0 2.0 35.0
>>END_MODULE
+>>Per tile sequence quality pass
+#Tile Base Mean
+1101 1 0.0
+1101 2 0.0
+1101 3 0.0
+1101 4 0.0
+1101 5 0.0
+1101 6 0.0
+1101 7 0.0
+1101 8 0.0
+1101 9 0.0
+1101 10-11 0.0
+1101 12-13 0.0
+1101 14-15 0.0
+1101 16-17 0.0
+1101 18-19 0.0
+1101 20-21 0.0
+1101 22-23 0.0
+1101 24-25 0.0
+1101 26-27 0.0
+1101 28-29 0.0
+1101 30-31 0.0
+1101 32-33 0.0
+1101 34-35 0.0
+1101 36-37 0.0
+1101 38-39 0.0
+1101 40-41 0.0
+1101 42-43 0.0
+1101 44-45 0.0
+1101 46-47 0.0
+1101 48-49 0.0
+1101 50-51 0.0
+1101 52-53 0.0
+1101 54-55 0.0
+1101 56-57 0.0
+1101 58-59 0.0
+1101 60-61 0.0
+1101 62-63 0.0
+1101 64-65 0.0
+1101 66-67 0.0
+1101 68-69 0.0
+1101 70-71 0.0
+1101 72-73 0.0
+1101 74-75 0.0
+1101 76-77 0.0
+1101 78-79 0.0
+1101 80-81 0.0
+1101 82-83 0.0
+1101 84-85 0.0
+1101 86-87 0.0
+1101 88-89 0.0
+1101 90-91 0.0
+1101 92-93 0.0
+1101 94-95 0.0
+1101 96-97 0.0
+1101 98-99 0.0
+1101 100 0.0
+>>END_MODULE
>>Per sequence quality scores pass
#Quality Count
11 1.0
@@ -99,57 +168,53 @@ Sequence length 100
7 20.9 24.7 32.6 21.8
8 20.0 27.200000000000003 30.0 22.8
9 24.5 21.5 27.800000000000004 26.200000000000003
-10-14 25.22 23.28 26.26 25.240000000000002
-15-19 26.44 21.34 26.1 26.119999999999997
-20-24 25.240000000000002 22.1 24.6 28.060000000000002
-25-29 24.62 22.06 25.119999999999997 28.199999999999996
-30-34 26.240000000000002 21.44 24.279999999999998 28.04
-35-39 24.8 22.439999999999998 24.34 28.42
-40-44 25.8 22.84 23.9 27.46
-45-49 26.26 22.64 23.66 27.439999999999998
-50-54 26.72 22.58 23.18 27.52
-55-59 25.019999999999996 22.58 24.38 28.02
-60-64 26.251501802162597 22.00640768922707 23.28794553464157 28.454144973968766
-65-69 25.683829444891394 23.873692679002414 23.049074818986323 27.39340305711987
-70-74 25.554134697357206 25.44757033248082 21.717817561807333 27.28047740835465
-75-79 25.818501428257523 23.643155350472423 23.071852340145025 27.466490881125026
-80-84 26.973532796317606 23.95857307249712 21.74913693901036 27.318757192174914
-85-89 25.452016689847014 24.849327770050998 22.624014835419565 27.07464070468243
-90-94 24.547101449275363 22.35054347826087 24.139492753623188 28.962862318840582
-95-99 25.318837549655026 24.231653773782146 23.186284758519758 27.263223918043067
+10-11 25.15 24.0 27.55 23.3
+12-13 26.200000000000003 22.3 24.65 26.85
+14-15 24.75 21.95 26.3 27.0
+16-17 25.4 21.7 26.55 26.35
+18-19 27.650000000000002 21.6 25.85 24.9
+20-21 24.8 21.8 24.3 29.099999999999998
+22-23 25.900000000000002 23.05 24.15 26.900000000000002
+24-25 24.85 21.4 25.900000000000002 27.85
+26-27 24.7 20.849999999999998 25.0 29.45
+28-29 24.4 23.3 24.95 27.35
+30-31 27.35 20.95 25.15 26.55
+32-33 24.9 22.05 23.400000000000002 29.65
+34-35 25.6 22.15 25.900000000000002 26.35
+36-37 24.95 21.2 23.400000000000002 30.45
+38-39 24.8 23.35 23.7 28.15
+40-41 27.0 23.35 23.599999999999998 26.05
+42-43 25.15 22.35 23.799999999999997 28.7
+44-45 26.200000000000003 20.7 24.3 28.799999999999997
+46-47 26.3 24.0 23.150000000000002 26.55
+48-49 25.5 23.3 24.05 27.150000000000002
+50-51 27.55 22.75 23.7 26.0
+52-53 24.45 23.400000000000002 23.1 29.049999999999997
+54-55 27.450000000000003 21.85 23.0 27.700000000000003
+56-57 25.85 22.15 23.5 28.499999999999996
+58-59 24.05 22.75 25.6 27.6
+60-61 25.25 20.95 23.45 30.349999999999998
+62-63 27.3 21.9 23.7 27.1
+64-65 26.178535606820464 24.57372116349047 22.617853560682047 26.629889669007024
+66-67 25.7 23.75 22.05 28.499999999999996
+68-69 25.405679513184587 23.52941176470588 24.036511156186613 27.028397565922923
+70-71 25.159574468085104 23.085106382978722 23.138297872340424 28.617021276595743
+72-73 26.031065881092662 26.513122656668454 20.51419389394751 26.941617568291377
+74-75 25.197680548234054 26.56826568265683 21.929362150764366 26.304691618344755
+76-77 25.911812738160044 23.51660315732172 24.550898203592812 26.02068590092542
+78-79 26.16345062429058 22.985244040862657 21.793416572077184 29.05788876276958
+80-81 26.98324022346369 25.474860335195533 21.005586592178773 26.536312849162012
+82-83 26.46370023419204 24.355971896955502 22.131147540983605 27.049180327868854
+84-85 26.124567474048444 23.18339100346021 22.145328719723185 28.546712802768166
+86-87 25.976331360946748 25.443786982248522 22.36686390532544 26.21301775147929
+88-89 25.503742084052966 23.54634427173287 23.316062176165804 27.63385146804836
+90-91 23.832052040212893 21.525724423418097 25.901833234772326 28.74039030159669
+92-93 24.525139664804467 22.849162011173185 23.743016759776538 28.88268156424581
+94-95 25.161987041036717 24.028077753779698 22.4622030237581 28.347732181425485
+96-97 25.37393162393162 24.412393162393162 23.664529914529915 26.549145299145298
+98-99 25.67703109327984 23.620862587763288 22.71815446339017 27.9839518555667
100 24.0 26.0 21.9 28.1
>>END_MODULE
->>Per base GC content fail
-#Base %GC
-1 71.01303911735206
-2 64.1
-3 73.3
-4 65.3
-5 55.800000000000004
-6 87.3
-7 42.699999999999996
-8 42.8
-9 50.7
-10-14 50.46000000000001
-15-19 52.559999999999995
-20-24 53.300000000000004
-25-29 52.82
-30-34 54.279999999999994
-35-39 53.22
-40-44 53.26
-45-49 53.7
-50-54 54.24
-55-59 53.04
-60-64 54.70564677613135
-65-69 53.07723250201126
-70-74 52.834612105711855
-75-79 53.28499230938255
-80-84 54.29228998849251
-85-89 52.526657394529444
-90-94 53.509963768115945
-95-99 52.5820614676981
-100 52.1
->>END_MODULE
>>Per sequence GC content fail
#GC Content Count
0 0.0
@@ -265,24 +330,51 @@ Sequence length 100
7 0.0
8 0.0
9 0.0
-10-14 0.0
-15-19 0.0
-20-24 0.0
-25-29 0.0
-30-34 0.0
-35-39 0.0
-40-44 0.0
-45-49 0.0
-50-54 0.0
-55-59 0.0
-60-64 0.12
-65-69 0.5599999999999999
-70-74 6.16
-75-79 8.98
-80-84 13.100000000000001
-85-89 13.719999999999999
-90-94 11.68
-95-99 4.34
+10-11 0.0
+12-13 0.0
+14-15 0.0
+16-17 0.0
+18-19 0.0
+20-21 0.0
+22-23 0.0
+24-25 0.0
+26-27 0.0
+28-29 0.0
+30-31 0.0
+32-33 0.0
+34-35 0.0
+36-37 0.0
+38-39 0.0
+40-41 0.0
+42-43 0.0
+44-45 0.0
+46-47 0.0
+48-49 0.0
+50-51 0.0
+52-53 0.0
+54-55 0.0
+56-57 0.0
+58-59 0.0
+60-61 0.0
+62-63 0.0
+64-65 0.3
+66-67 0.0
+68-69 1.4000000000000001
+70-71 6.0
+72-73 6.65
+74-75 5.1499999999999995
+76-77 8.15
+78-79 11.899999999999999
+80-81 10.5
+82-83 14.6
+84-85 13.3
+86-87 15.5
+88-89 13.15
+90-91 15.45
+92-93 10.5
+94-95 7.3999999999999995
+96-97 6.4
+98-99 0.3
100 0.0
>>END_MODULE
>>Sequence Length Distribution pass
@@ -290,565 +382,85 @@ Sequence length 100
100 1000.0
>>END_MODULE
>>Sequence Duplication Levels pass
-#Total Duplicate Percentage 3.4
-#Duplication Level Relative count
-1 100.0
-2 0.4140786749482402
-3 0.0
-4 0.0
-5 0.0
-6 0.0
-7 0.0
-8 0.0
-9 0.0
-10++ 0.2070393374741201
+#Total Deduplicated Percentage 97.2
+#Duplication Level Percentage of deduplicated Percentage of total
+1 99.38271604938271 96.6
+2 0.411522633744856 0.8
+3 0.0 0.0
+4 0.0 0.0
+5 0.0 0.0
+6 0.0 0.0
+7 0.0 0.0
+8 0.0 0.0
+9 0.0 0.0
+>10 0.205761316872428 2.6
+>50 0.0 0.0
+>100 0.0 0.0
+>500 0.0 0.0
+>1k 0.0 0.0
+>5k 0.0 0.0
+>10k+ 0.0 0.0
>>END_MODULE
>>Overrepresented sequences fail
#Sequence Count Percentage Possible Source
-AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTAT 14 1.4000000000000001 TruSeq Adapter, Index 1 (97% over 36bp)
-GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATG 12 1.2 TruSeq Adapter, Index 1 (97% over 36bp)
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTAT 14 1.4000000000000001 TruSeq Adapter, Index 18 (97% over 37bp)
+GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATG 12 1.2 TruSeq Adapter, Index 18 (97% over 37bp)
AGGGGGAATGATGGTTGTCTTTGGATATACTACAGCGATGGCTATTGAGG 2 0.2 No Hit
GGCTTGTTTTATTTTAATGGCTGATCTATGTAATCACAGAGGCCAGTATG 2 0.2 No Hit
GTGGGGTGGTGTTTGTGGGGGACTTCATCATCTCAGGCTTCCCAGGGTCC 2 0.2 No Hit
-CGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATGCCG 2 0.2 TruSeq Adapter, Index 1 (96% over 33bp)
+CGGAAGAGCACACGTCTGAACTCCAGTCACTTCCAAGATCTCGTATGCCG 2 0.2 TruSeq Adapter, Index 18 (97% over 34bp)
+>>END_MODULE
+>>Adapter Content fail
+#Position Illumina Universal Adapter Illumina Small RNA Adapter Nextera Transposase Sequence
+1 1.4 0.0 0.0
+2 1.4 0.0 0.0
+3 1.4 0.0 0.0
+4 1.4 0.0 0.0
+5 1.4 0.0 0.0
+6 1.4 0.0 0.0
+7 1.4 0.0 0.0
+8 1.4 0.0 0.0
+9 1.4 0.0 0.0
+10-11 1.4 0.0 0.0
+12-13 1.4 0.0 0.0
+14-15 1.4 0.0 0.0
+16-17 1.4 0.0 0.0
+18-19 1.4 0.0 0.0
+20-21 1.5 0.0 0.0
+22-23 1.5 0.0 0.0
+24-25 1.5 0.0 0.0
+26-27 1.5 0.0 0.0
+28-29 1.6 0.0 0.0
+30-31 1.7 0.0 0.0
+32-33 1.9 0.0 0.0
+34-35 2.4 0.0 0.0
+36-37 2.45 0.0 0.0
+38-39 2.95 0.0 0.0
+40-41 3.25 0.0 0.0
+42-43 3.75 0.0 0.0
+44-45 4.2 0.0 0.0
+46-47 4.9 0.0 0.0
+48-49 5.699999999999999 0.0 0.0
+50-51 6.300000000000001 0.0 0.0
+52-53 6.949999999999999 0.0 0.0
+54-55 7.65 0.0 0.0
+56-57 8.399999999999999 0.0 0.0
+58-59 9.350000000000001 0.0 0.0
+60-61 9.899999999999999 0.0 0.0
+62-63 10.600000000000001 0.0 0.0
+64-65 11.3 0.0 0.0
+66-67 12.0 0.0 0.0
+68-69 13.05 0.0 0.0
+70-71 13.6 0.0 0.0
+72-73 14.5 0.0 0.0
+74-75 15.55 0.0 0.0
+76-77 16.15 0.0 0.0
+78-79 17.2 0.0 0.0
+80-81 17.700000000000003 0.0 0.0
+82-83 18.15 0.0 0.0
+84-85 18.75 0.0 0.0
+86-87 19.799999999999997 0.0 0.0
+88 20.6 0.0 0.0
>>END_MODULE
->>Kmer Content fail
-#Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
-AAAAA 385 7.3597403 68.038994 65-69
-AGATC 435 5.4375157 23.135067 1
-GAAGA 375 5.258809 32.443344 6
-GGAAG 420 5.044668 33.345257 5
-TCCAG 475 4.8355613 14.131038 2
-AAGAG 320 4.487517 25.954676 7
-CCAGG 475 4.4180827 17.21471 3
-GAGCA 380 4.3399205 21.1377 9
-AGCAC 395 4.2895336 15.0741825 7
-CTCCA 415 4.0171337 12.105032 95-96
-AGAGC 340 3.883087 21.137697 8
-TTTTT 280 3.8749053 8.964593 10-14
-CTTCT 370 3.8646336 11.598914 55-59
-CTGAA 305 3.812511 13.130004 90-94
-CGGAA 320 3.65467 26.422123 5
-ACCAG 335 3.6379597 10.049457 7
-TCTGA 310 3.6325634 12.308498 90-94
-CACAC 340 3.5108058 14.806036 85-89
-ATCGG 325 3.4795394 24.768969 3
-TCGGA 320 3.426008 19.815174 3
-GATCG 320 3.426008 19.815174 1
-CGTCT 355 3.387832 11.578538 85-89
-CTGCT 355 3.387832 17.662533 3
-GCACA 310 3.3664696 15.0741825 8
-TCTTC 320 3.3423858 7.7326093 50-54
-CAGCA 305 3.3121717 10.049455 6
-GAACT 260 3.2500093 13.130004 90-94
-GTCTG 320 3.2116532 12.65067 90-94
-CAGGA 280 3.197836 15.8532715 3
-AACTC 265 3.1497202 23.781752 95-96
-TGAAC 250 3.125009 13.130004 90-94
-CCAGC 350 3.0954454 6.6359653 95-96
-AGTCA 240 3.0000086 10.41078 25-29
-CACCA 290 2.9945107 6.079907 70-74
-TGCTG 295 2.960743 9.2877 2
-CAGAT 230 2.875008 11.040063 70-74
-CTTCC 315 2.8583732 10.916445 30-34
-CACGT 280 2.8504362 12.351324 85-89
-CAGGG 290 2.8367646 22.630535 9
-ACACG 260 2.8234906 13.175687 85-89
-TTCCA 250 2.7855206 9.279795 30-34
-TTCTT 230 2.765239 6.6755276 50-54
-AGCAG 240 2.7410026 15.853272 2
-TTCTG 240 2.6363494 10.165324 55-59
-ACTCC 270 2.6135564 14.526036 95-96
-GCCAG 280 2.6043434 8.607355 1
-ACGTC 255 2.595933 10.105629 85-89
-GATCT 220 2.5779483 8.675031 40-44
-TCTGC 265 2.5289452 13.2469015 2
-AAGAT 160 2.4557784 12.783248 35-39
-ATCTC 220 2.4512577 9.279794 40-44
-CAGTC 240 2.4432309 8.554544 90-94
-TCCAA 205 2.4365761 10.999062 7
-CTTTT 200 2.4045558 16.688818 6
-TTCCT 230 2.40234 9.665762 7
-CCAGT 235 2.3923304 9.4206915 25-29
-TTTCT 195 2.3444414 16.688818 8
-CTGGG 255 2.3383298 6.004135 80-84
-TGCTT 210 2.3068056 10.165323 4
-TCTTT 190 2.284328 5.5629396 15-19
-TTTTC 190 2.2843277 11.125878 7
-GGGGG 255 2.2468696 16.307867 2
-AGGAA 160 2.2437584 19.466007 5
-GTCAC 220 2.2396283 10.184532 95-96
-TCACT 200 2.2284167 8.360176 95-96
-CACTT 200 2.2284167 10.3108835 30-34
-GAAAA 135 2.2103586 10.606119 60-64
-ACTTC 195 2.172706 9.279794 30-34
-TTGAA 150 2.1582448 11.9834385 60-64
-CTCCT 235 2.1324375 16.794533 4
-TCCTC 235 2.1324372 8.397265 5
-ATCTT 165 2.11616 7.1210704 10-14
-GGGGA 205 2.1089406 14.2801 3
-ACACA 165 2.092039 11.7331705 8
-TGCAG 195 2.0877237 9.907587 5
-GACCA 190 2.0633202 10.049455 6
-AGGGG 200 2.057503 9.520067 1
-CCTCC 260 2.049668 14.590484 5
-AGGAG 170 2.0418897 5.557543 2
-TCCTT 195 2.0367663 14.498643 4
-GTCTT 185 2.032186 15.247986 7
-GCTGG 220 2.0173824 8.485845 1
-CCAGA 185 2.0090222 5.3284492 70-74
-CCTGG 230 2.0054333 8.068818 3
-GCAGG 205 2.005299 9.052214 3
-GGACC 215 1.9997637 8.607355 5
-TTCAT 155 1.987908 5.934226 2
-CCTTT 190 1.9845415 14.498643 5
-TTTCC 190 1.9845415 5.799457 15-19
-TGGCA 185 1.980661 14.861383 2
-TCTTG 180 1.977262 10.165323 5
-CCAAG 180 1.9547247 9.044511 35-39
-CTTCA 175 1.9498644 10.310883 6
-CAAGA 145 1.933477 12.339583 35-39
-CTGGA 180 1.9271295 9.907587 6
-GGCTG 210 1.9256833 16.97169 2
-AATGA 125 1.918577 7.677627 95-96
-TGAAA 125 1.918577 15.623971 60-64
-GCTTC 200 1.9086379 13.2469015 2
-GTCCA 185 1.8833237 14.131036 1
-AGAAA 115 1.882898 7.5757995 7
-TGGGG 195 1.8805519 13.386638 1
-TTCTC 180 1.880092 5.799457 25-29
-CTTGA 160 1.8748715 8.675031 60-64
-ACAAA 120 1.8682072 5.762797 40-44
-TCTCG 195 1.8609219 8.831266 5
-GGGAC 190 1.8585701 9.052216 5
-TGAGG 165 1.8578365 5.209824 2
-TGAAG 140 1.8404517 6.082693 2
-CATCT 165 1.8384434 5.155441 4
-CACTG 180 1.8324232 9.4206915 6
-CTGCA 180 1.8324231 5.3465896 90-94
-GCTGC 210 1.8310483 8.068819 1
-GCAGA 160 1.8273348 10.568848 3
-CCTTC 200 1.8148402 8.397265 9
-AGGGA 150 1.8016673 6.0081544 95-96
-TTTCA 140 1.7955297 7.1210704 15-19
-CACAG 165 1.7918309 5.432139 95-96
-AAACA 115 1.7903653 7.6389136 70-74
-ATTTT 120 1.7715117 13.661307 6
-TTTTG 140 1.7701824 17.551357 7
-GGGGC 210 1.7594293 11.629828 3
-GATTT 130 1.7534488 12.481857 6
-CAAAT 120 1.7513192 6.7527947 50-54
-GAGGG 170 1.7488776 9.520067 1
-GAAGG 145 1.7416117 6.0081544 95-96
-CATTT 135 1.7314036 5.9342256 5
-ATTTC 135 1.7314036 5.9342256 7
-CCTCT 190 1.7240983 8.397266 1
-ATCCA 145 1.7234317 5.49953 4
-GCAGC 185 1.7207267 6.9789357 95-96
-TCCTG 180 1.717774 13.2469 2
-CTCTG 180 1.717774 13.2469 2
-AAAAC 110 1.7125233 7.6389136 70-74
-CTTGG 170 1.7061908 9.2877 2
-AAAAT 95 1.7024158 8.291661 9
-TCACC 175 1.693972 8.957724 8
-TCCAC 175 1.693972 8.957724 5
-GAGAA 120 1.6828189 6.488669 6
-TCTCC 185 1.6787271 5.038359 55-59
-GAGCC 180 1.6742208 8.607355 9
-TCATC 150 1.6713123 5.1554413 2
-AGACA 125 1.6667906 6.169792 2
-TGATG 135 1.6636823 11.404236 9
-GGGAG 160 1.6460025 9.520067 1
-AGCCA 150 1.6289369 6.029673 10-14
-ATGCC 160 1.6288207 8.478622 45-49
-CTCGT 170 1.6223421 8.831266 3
-GAGGA 135 1.6215005 11.115086 3
-TGTTG 140 1.6173534 10.690706 2
-CTCAT 145 1.6156021 5.1554418 2
-CAGGT 150 1.6059413 9.907587 4
-GCTTG 160 1.6058266 9.2877 60-64
-GGGTC 175 1.6047363 12.728768 2
-TCATT 125 1.6031516 5.934226 9
-GTTGA 130 1.6020645 5.702118 1
-ACAGA 120 1.6001189 10.005068 95-96
-GGAGG 155 1.5945649 9.520067 2
-GGGGT 165 1.5912362 13.386638 1
-TGGGA 140 1.5763463 10.419649 2
-GGATG 140 1.5763462 15.629472 6
-GCCTC 190 1.575248 7.672287 2
-CCTGC 190 1.5752479 11.508429 2
-GCTCC 190 1.5752479 11.508429 6
-TCTCT 150 1.5667434 5.224736 95-96
-GGGAA 130 1.561445 11.115086 4
-TCCAT 140 1.5598917 10.3108835 8
-GGCTT 155 1.5556445 13.93155 1
-TTGAT 115 1.5511277 6.240928 4
-CATCA 130 1.5451456 5.49953 2
-AGAGA 110 1.542584 6.488669 9
-AGGAC 135 1.541814 6.341309 55-59
-GTATG 125 1.5404466 9.123388 45-49
-AACAT 105 1.5324043 13.5055895 9
-AGCTC 150 1.5270194 9.4206915 5
-TTTGT 120 1.5172992 17.551357 8
-GATGA 115 1.5117996 6.082693 5
-GAGAT 115 1.5117996 6.082693 4
-AGGAT 115 1.5117996 12.165386 4
-TGAGA 115 1.5117996 6.082693 5
-CTGGT 150 1.5054625 9.2877 4
-GCTGT 150 1.5054625 18.5754 3
-TTCAC 135 1.504181 10.310883 7
-CCCAG 170 1.5035021 12.276537 2
-CAGTG 140 1.4988785 9.907587 5
-CTCCC 190 1.4978343 7.295242 1
-CCCTG 180 1.4923402 11.5084305 2
-CAGAG 130 1.4847097 7.398194 20-24
-CTTTG 135 1.4829465 10.165323 2
-CAAAA 95 1.4789973 7.203496 9
-TCTCA 130 1.4484707 5.1554413 8
-GAATG 110 1.4460692 12.165386 7
-GGAAT 110 1.4460692 12.165386 5
-TTTGG 125 1.4440656 5.345353 7
-GGCCT 165 1.4386805 12.103227 1
-GCTCT 150 1.4314783 6.1818867 20-24
-TCTGT 130 1.4280226 15.247986 3
-CTGTT 130 1.4280226 15.247986 4
-AGGTT 115 1.4172109 11.404235 8
-TTGAG 115 1.4172107 5.702117 4
-TTTGA 105 1.416247 7.4891143 10-14
-ATCTG 120 1.4061534 5.4218936 2
-GGTCT 140 1.4050984 9.287701 6
-TTTTA 95 1.4024467 7.384491 95-96
-GGGTG 145 1.3983592 13.386638 2
-GGCAC 150 1.3951839 8.607355 4
-AAAGA 85 1.3917071 7.5757985 8
-AAGAA 85 1.3917071 5.254889 75-79
-TTGTT 110 1.3908576 5.850453 4
-GGAGA 115 1.3812783 5.557543 3
-ATGAC 110 1.3750039 6.252721 95-96
-TGTTC 125 1.3730987 10.165325 5
-GGGCA 140 1.3694727 9.052216 4
-ATGAT 95 1.3668885 6.6574664 6
-CCACT 140 1.3551775 5.3746343 30-34
-TGGCT 135 1.3549163 13.931552 3
-GATGG 120 1.3511539 10.419648 9
-TCGTA 115 1.3475639 5.421894 40-44
-TGTCA 115 1.3475639 5.421894 5
-GCTGA 125 1.3382844 9.907587 6
-CAGAA 100 1.3334324 5.6025352 90-94
-CCAAA 105 1.3312978 5.8665853 8
-GGGCT 145 1.3296387 12.728768 1
-TAGGA 100 1.3146083 12.165386 4
-GACAG 115 1.313397 5.2844243 1
-GGTCC 150 1.3078917 8.068819 6
-CCATC 135 1.3067783 8.957724 9
-AAATG 85 1.3046323 7.101804 6
-TTCAA 95 1.2997144 6.330293 9
-CGTAT 110 1.2889742 8.675031 45-49
-TGACT 110 1.2889742 5.421894 3
-TATGC 110 1.2889739 8.67503 45-49
-GCCCT 155 1.2850707 7.672287 3
-TGGGC 140 1.283789 8.485846 7
-ACTTT 100 1.2825212 5.9342256 1
-ATGTT 95 1.2813665 6.2409286 1
-ATTTG 95 1.2813663 12.481856 9
-TGGTT 110 1.2707777 5.345353 5
-TGGTG 120 1.2666163 9.767722 7
-GTTTT 100 1.2644161 5.8504534 6
-GCCTG 145 1.2642952 12.103229 1
-TTGCT 115 1.2632507 6.0991945 50-54
-CCACC 150 1.2614243 7.7821474 5
-GGACA 110 1.2562928 15.853274 6
-GAAGC 110 1.2562928 10.568849 9
-TGACA 100 1.2500036 5.7837667 9
-GACAT 100 1.2500035 11.567533 7
-TGGAA 95 1.248878 6.082693 5
-ACAGC 115 1.2488517 10.049455 5
-AATCC 105 1.2480024 5.499531 7
-TGCCT 130 1.2406145 8.831266 3
-AGGTG 110 1.2385577 5.209824 4
-GTGGC 135 1.2379395 12.728768 1
-CATGT 105 1.2303842 5.4218936 1
-TAGAT 85 1.2230055 6.0453725 90-94
-CCCTC 155 1.2219174 7.295242 4
-GCCGT 140 1.2206988 8.068819 3
-AGTTT 90 1.2139261 6.2409286 7
-TTTAG 90 1.213926 6.240928 8
-TTGGG 115 1.2138406 9.767722 2
-ACCTC 125 1.20998 8.957724 1
-AGCAA 90 1.2000892 6.169792 9
-CAAAG 90 1.2000891 6.169791 5
-AAAGC 90 1.2000891 6.169791 6
-ACAGG 105 1.1991886 10.568849 8
-AGGCA 105 1.1991886 5.712891 95-96
-ATCAG 95 1.1875033 5.7837663 6
-ATGAG 90 1.1831475 6.082693 25-29
-CAGTT 100 1.1717947 5.1698627 85-89
-ATGCT 100 1.1717947 5.421894 8
-TCAAT 85 1.1629024 6.3302937 10-14
-TGTGT 100 1.1552525 10.690706 3
-GCCCA 130 1.1497369 12.276536 1
-TGATT 85 1.1464858 12.481857 5
-TGCTC 120 1.1451827 8.831267 4
-TGTCC 120 1.1451827 13.2469015 2
-TCCCC 145 1.143084 7.295242 2
-AAGGC 100 1.1420842 5.493164 65-69
-CAACA 90 1.1411123 5.8665853 8
-CACAA 90 1.1411123 11.7331705 9
-ACATC 95 1.129145 5.4995303 8
-AAGCT 90 1.1250031 6.2527194 95-96
-GAAAG 80 1.1218792 12.977338 7
-AAGGA 80 1.1218792 6.488669 3
-GCACT 110 1.1198142 9.4206915 5
-CCTGA 110 1.119814 9.420691 9
-ACCTT 100 1.1142083 5.1554418 7
-GTCAT 95 1.113205 5.421894 1
-TGATC 95 1.113205 10.843788 5
-TCATG 95 1.113205 5.421894 3
-TGGAT 90 1.1091216 5.702118 9
-GTGGG 115 1.1090435 8.924425 1
-CTGTG 110 1.1040058 9.2877 4
-GCTTT 100 1.0984789 5.4947696 95-96
-TGTCT 100 1.0984789 10.165323 5
-TTGGT 95 1.0974898 5.345353 4
-CTGTC 115 1.0974668 17.662535 4
-CAGAC 100 1.0859579 5.0247273 5
-GGAAC 95 1.0849801 5.2844243 6
-CCTCG 130 1.0778012 7.672287 6
-GCGGC 135 1.075477 7.372196 1
-ATAAA 60 1.0752101 8.291662 7
-GGGAT 95 1.0696635 10.419649 3
-CATCC 110 1.0647823 8.957723 3
-ACAGT 85 1.062503 5.7837663 4
-ACTGA 85 1.062503 11.567533 7
-GTTGG 100 1.0555136 9.767722 1
-TGTGG 100 1.0555136 9.767722 5
-GGAAA 75 1.0517617 19.466007 6
-GTGAA 80 1.0516868 6.082693 1
-GAAGT 80 1.0516866 6.082693 5
-GTCTC 110 1.0497508 8.831267 1
-CGGCT 120 1.046313 8.068818 1
-TTTAT 70 1.0333818 5.4645233 10-14
-GACAC 95 1.0316601 10.049455 7
-GGCAA 90 1.0278759 10.56885 3
-TCATA 75 1.0260904 6.330293 5
-ATTCA 75 1.0260903 6.3302927 7
-TAACA 70 1.0216029 6.7527957 8
-GGTCA 95 1.0170963 9.907589 3
-ATGGC 95 1.0170962 9.907587 1
-TCAGG 95 1.0170962 9.907587 8
-GGTGA 90 1.0133655 15.629474 3
-TGTTT 80 1.0115329 5.8504534 5
-TGAAT 70 1.007181 6.6574664 5
-ATTGA 70 1.0071809 6.6574664 7
-AAGTT 70 1.0071809 6.6574664 6
-TTGCC 105 1.0020349 8.831267 2
-CTTGC 105 1.0020349 8.831267 6
-GCAAA 75 1.0000744 6.169792 4
-CATAG 80 1.0000029 6.2527204 95-96
-GACTT 85 0.99602544 5.421894 1
-CTGAT 85 0.99602544 5.421894 4
-CTTGT 90 0.988631 10.165323 3
-AATGG 75 0.98595625 6.082693 8
-AAGGT 75 0.9859562 6.0826926 4
-GATGT 80 0.98588586 5.7021174 7
-GGATT 80 0.98588586 11.404235 5
-GGCGG 115 0.96349704 7.753219 1
-AGAGG 80 0.9608892 5.557543 8
-GAGGT 85 0.95706743 5.2098246 3
-ATGGG 85 0.9570673 5.209824 1
-CCGTC 115 0.95343953 7.672287 4
-TAGCA 75 0.9375027 5.7837667 1
-ACATG 75 0.9375026 5.7837663 2
-TTGCA 80 0.93743575 5.421894 4
-GTTCA 80 0.93743575 5.421894 6
-ATGTC 80 0.93743575 5.421894 5
-TTCAG 80 0.93743575 5.421894 8
-TTGAC 80 0.9374356 5.4218936 2
-GTTCT 85 0.93370706 5.0826616 1
-TTGTC 85 0.93370706 5.0826616 9
-TTTGC 85 0.93370706 5.0826616 3
-ATGGT 75 0.924268 5.7021174 4
-ATGAA 60 0.920917 7.1018047 9
-AGATG 70 0.92022586 6.082693 5
-GCTCA 90 0.91621155 5.092265 95-96
-AGTGC 85 0.9100334 9.907587 2
-AGGGT 80 0.90076935 10.419649 1
-GTAGG 80 0.90076923 10.419648 6
-AGTGG 80 0.90076923 5.209824 2
-TAAAA 50 0.89600843 8.291662 8
-CACAT 75 0.89143026 5.499531 6
-CCATT 80 0.89136666 10.3108835 9
-ATACT 65 0.8892783 6.330293 9
-ACATT 65 0.88927823 6.3302927 7
-GCGGG 105 0.87971467 7.753219 2
-ACACC 85 0.8777014 9.555587 9
-CATAA 60 0.8756596 6.7527947 6
-ACCCT 90 0.8711856 13.436585 1
-GAACA 65 0.8667311 6.169792 7
-ACTGC 85 0.8653109 5.092265 95-96
-GGTAT 70 0.86265016 17.106354 6
-AGTTG 70 0.86265016 5.702118 7
-GAGAC 75 0.85656327 5.2844243 1
-GTGTC 85 0.8530954 13.93155 1
-GTTGC 85 0.8530954 9.2877 1
-ATAGA 55 0.84417385 7.1018047 8
-GAAAT 55 0.84417385 7.1018047 5
-CATTC 75 0.83565605 5.155441 6
-TCACA 70 0.83200157 5.499531 3
-TGCGG 90 0.8252928 8.485845 3
-GCATT 70 0.8202563 5.421894 4
-GAACC 75 0.8144686 5.0247283 6
-CTCGA 80 0.81441027 9.420691 6
-GAATC 65 0.8125023 5.7837667 6
-TACAG 65 0.81250226 11.567533 7
-TGGTA 65 0.80103225 11.404236 5
-AAGAC 60 0.80005944 6.169791 8
-CAAGG 70 0.7994591 5.2844243 2
-ATGTA 55 0.7913565 6.6574664 4
-AATGT 55 0.7913565 6.6574664 3
-CGGCA 85 0.7906042 8.607354 2
-GAGAG 65 0.7807225 5.557543 8
-ACCAT 65 0.7725729 5.499531 8
-TTCTA 60 0.7695128 5.934226 9
-TAGAA 50 0.7674308 7.1018047 9
-GCATC 75 0.7635097 9.4206915 1
-GTTCC 80 0.76345515 8.831267 6
-AGCTT 65 0.76166654 5.421894 1
-TTAGC 65 0.76166654 5.421894 9
-CTGTA 65 0.76166654 5.421894 2
-ACTTG 65 0.7616664 5.4218936 2
-GTGCT 75 0.7527313 9.287701 3
-ATCAT 55 0.7524662 6.3302927 3
-GTTTG 65 0.7509141 5.345353 9
-GTGTT 65 0.7509141 10.690706 1
-GTCAA 60 0.75000215 11.5675335 6
-AATGC 60 0.75000215 6.252721 95-96
-CAAGT 60 0.7500021 5.7837663 9
-GCAAT 60 0.7500021 5.7837663 4
-GCAAG 65 0.74235487 5.2844243 1
-AGTGT 60 0.7394144 5.7021174 1
-TTAGG 60 0.7394144 5.702118 7
-AGCGG 75 0.73364604 9.052214 1
-ATCCT 65 0.72423524 5.155441 4
-ACTCT 65 0.72423524 5.155441 9
-AGTGA 55 0.7230346 6.082693 6
-AATAA 40 0.71680677 8.291662 6
-AACCT 60 0.71314424 5.4995303 1
-ATTCT 55 0.70538664 5.9342256 7
-AGTCT 60 0.7030768 5.421894 3
-GTGCA 65 0.69590795 9.907589 6
-AAAGT 45 0.69068766 7.101804 8
-AACTG 55 0.6875019 5.7837663 1
-CGAAG 60 0.68525064 5.2844243 4
-GATTG 55 0.67779654 5.702118 6
-GTGAT 55 0.67779654 11.404236 4
-TGTTA 50 0.67440337 12.481857 5
-TTGTA 50 0.6744033 6.240928 9
-TATTG 50 0.6744033 6.240928 7
-CTCTA 60 0.6685249 5.1554413 7
-TACCT 60 0.66852486 10.310882 8
-ATGGA 50 0.65730417 6.082693 8
-ATACA 45 0.6567447 6.7527957 6
-ATCAA 45 0.65674466 6.7527947 9
-TGTAA 45 0.6474735 6.6574664 7
-GCGGT 70 0.6418945 8.485846 4
-GGCCG 80 0.63731974 7.372196 2
-GGTTT 55 0.63538885 10.690706 9
-TTGTG 55 0.63538885 5.345353 1
-TATAT 40 0.62991583 7.2865515 8
-CCTGT 65 0.62030727 8.831266 3
-GTGAG 55 0.6192789 5.2098246 1
-TAGGG 55 0.61927885 5.209824 8
-GAGTT 50 0.6161787 5.7021174 6
-ATGTG 50 0.6161787 5.702118 2
-GAATA 40 0.61394465 7.1018047 6
-CTGCG 70 0.6103493 8.068818 2
-CGGTG 65 0.59604484 8.485845 2
-TAAGG 45 0.5915738 6.082693 9
-AAGTG 45 0.5915737 6.0826926 1
-TATTT 40 0.5905039 6.8306537 8
-GGCAT 55 0.5888452 14.861383 3
-GTATC 50 0.5858973 5.421894 4
-ATAAC 40 0.5837731 13.505591 7
-TTACT 45 0.57713455 5.934226 9
-GTATA 40 0.575532 13.314933 7
-GAGTG 50 0.5629808 5.209824 1
-GTACA 45 0.5625016 5.7837667 6
-ATAGC 45 0.5625016 5.7837667 9
-TCTAC 50 0.5571041 5.1554413 8
-GCGAG 55 0.53800714 9.052216 1
-ACGGG 55 0.5380071 9.052214 1
-GATAA 35 0.5372016 7.1018047 6
-AATAG 35 0.5372016 7.101805 7
-CAACT 45 0.53485817 5.4995303 6
-CATAC 45 0.53485817 5.4995303 5
-GATTC 45 0.52730757 5.421894 6
-AGGTA 40 0.5258433 12.165386 5
-CGGTC 60 0.52315664 8.068819 5
-ACGAG 45 0.51393795 5.2844243 7
-TATTC 40 0.5130085 5.9342256 7
-CTAAA 35 0.51080143 6.7527957 9
-TACAA 35 0.51080143 5.402236 35-39
-CCTTA 45 0.5013937 5.1554413 6
-CAGTA 40 0.50000143 5.7837667 4
-GTGTA 40 0.49294293 5.702118 4
-TAACT 35 0.47884214 6.330293 8
-CTTAA 35 0.47884214 6.330293 7
-CTATA 35 0.47884214 6.330293 4
-TTAAC 35 0.47884214 6.330293 8
-TATCA 35 0.4788421 6.3302927 5
-TCAAC 40 0.47542948 5.499531 7
-ACTCA 40 0.47542942 5.49953 8
-TTAGT 35 0.47208238 10.120425 95-96
-TGTAT 35 0.47208238 6.2409286 3
-ATTGT 35 0.47208235 6.240928 8
-GTTAC 40 0.46871787 5.421894 6
-TGTAC 40 0.46871787 10.843788 7
-AGAGT 35 0.46011293 6.082693 5
-AGTAG 35 0.46011293 6.082693 5
-CTCCG 55 0.45599285 7.672287 6
-GGTAG 40 0.45038468 5.2098246 2
-TTTAC 35 0.44888243 5.9342256 8
-CTACT 40 0.44568333 5.1554418 4
-AACTA 30 0.4378298 6.7527947 9
-TATAG 30 0.43164897 6.6574664 5
-ATATA 25 0.4199739 7.7728767 9
-CTCAA 35 0.41600078 5.499531 9
-TATAC 30 0.4104361 6.3302927 5
-ACTAT 30 0.4104361 6.3302927 6
-TACTA 30 0.4104361 6.3302927 5
-TCGAT 35 0.41012815 10.843788 7
-ACGTT 35 0.41012815 5.421894 4
-CGAAA 30 0.40002972 6.169792 9
-GTAAG 30 0.3943825 6.082693 8
-ATAGG 30 0.3943825 6.082693 3
-TCCTA 35 0.38997287 5.1554413 5
-TTACC 35 0.38997287 5.1554413 7
-ACCGA 35 0.3800853 5.0247273 7
-GCATA 30 0.37500107 5.7837667 1
-TCGAA 30 0.37500107 5.7837667 4
-GCTAA 30 0.37500107 5.7837667 8
-TAGGT 30 0.3697072 5.7021174 7
-GTTAG 30 0.3697072 5.702118 6
-CAATA 25 0.36485815 6.7527947 5
-ATACC 30 0.35657212 5.499531 6
-GACGA 30 0.3426253 5.284424 6
-AAGCG 30 0.3426253 10.568848 7
-GTTTA 25 0.33720168 6.2409286 7
-GTATT 25 0.33720168 12.481857 6
-AGATA 20 0.30697232 7.1018047 5
-CGTCA 30 0.30540386 9.420691 5
-CCTAA 25 0.29714343 5.499531 7
-TACCA 25 0.2971434 5.49953 9
-TGCTA 25 0.29294866 5.421894 7
-TACGT 25 0.29294863 5.4218936 9
-AGACG 25 0.2855211 5.284425 9
-CCTAT 25 0.2785521 5.1554418 3
-TAAGC 20 0.25000072 5.7837667 9
-CTAAG 20 0.25000072 5.7837667 8
-CGATT 20 0.23435894 5.421894 9
-GGGTA 20 0.22519234 5.2098246 2
-ACGCA 20 0.21719159 5.0247273 5
-GCGAA 15 0.17131266 5.284425 3
-CGAAC 15 0.16289368 5.0247273 5
+>>Kmer Content pass
>>END_MODULE
diff --git a/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..2b537d9767cbc1ddbd9f2e528a1c122dfe973d7c
--- /dev/null
+++ b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala
@@ -0,0 +1,84 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import org.testng.annotations.Test
+
+class CutadaptTest extends FastqcV0101Test {
+ /** Mock output file of a Cutadapt 1.9 run */
+ private[flexiprep] val cutadaptOut: File = resourceFile("ct-test.R1.clip.stats")
+
+ def testFastQCinstance: Fastqc = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+ fqc.contaminants = Option(resourceFile("fqc_contaminants_v0112.txt"))
+ // fqc.beforeGraph()
+ fqc
+ }
+
+ def testCutadaptInst: Cutadapt = {
+ val caExe = new Cutadapt(null, testFastQCinstance)
+ caExe.statsOutput = cutadaptOut
+ caExe
+ }
+
+ @Test def testAdapterFound() = {
+ val cutadapt = testCutadaptInst
+ val adapters = cutadapt.extractClippedAdapters(cutadaptOut)
+ adapters.keys.size shouldBe 4
+
+ adapters.get("CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC") shouldBe Some(
+ Map(
+ "count" -> 94,
+ "histogram" -> Map(
+ "5p" -> Map(5 -> 2, 6 -> 4, 9 -> 1, 3 -> 8, 4 -> 3),
+ "3p" -> Map(5 -> 21, 6 -> 18, 9 -> 1, 12 -> 1, 7 -> 2, 3 -> 13, 11 -> 1, 4 -> 19)
+ )
+ )
+ )
+
+ adapters.get("CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC") shouldBe Some(
+ Map(
+ "count" -> 0,
+ "histogram" -> Map()
+ )
+ )
+ }
+
+ @Test def testSummary() = {
+ val cutadapt = testCutadaptInst
+ val summary = cutadapt.summaryStats
+
+ summary.keys shouldBe Set("num_bases_input", "num_reads_input", "num_reads_output",
+ "num_reads_with_adapters", "num_reads_affected", "num_reads_discarded_too_long",
+ "adapters", "num_reads_discarded_many_n", "num_reads_discarded_too_short", "num_bases_output")
+
+ summary.keys.size shouldBe 10
+ summary("adapters").asInstanceOf[Map[String, Map[String, Any]]].keys.size shouldBe 4
+
+ summary("num_bases_input") shouldBe 100000
+ summary("num_reads_input") shouldBe 1000
+ summary("num_reads_output") shouldBe 985
+ summary("num_reads_with_adapters") shouldBe 440
+ summary("num_reads_affected") shouldBe 425
+ summary("num_reads_discarded_too_long") shouldBe 0
+ summary("num_reads_discarded_many_n") shouldBe 0
+ summary("num_reads_discarded_too_short") shouldBe 15
+ summary("num_bases_output") shouldBe 89423
+ }
+}
diff --git a/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
index 4cb68fdfc44d5a30c3ed76aabc9570d6f62529f3..3cf24e8c60a570e8e51fe528ece4f81d0b66a01a 100644
--- a/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
+++ b/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala
@@ -25,14 +25,14 @@ import org.testng.annotations.Test
class FastqcV0101Test extends TestNGSuite with Matchers {
/** Returns the absolute path to test resource directory as a File object */
- private val resourceDir: File = new File(Paths.get(getClass.getResource("/").toURI).toString)
+ private[flexiprep] val resourceDir: File = new File(Paths.get(getClass.getResource("/").toURI).toString)
/** Given a resource file name, returns the the absolute path to it as a File object */
- private def resourceFile(p: String): File = new File(resourceDir, p)
+ private[flexiprep] def resourceFile(p: String): File = new File(resourceDir, p)
/** Mock output file of a FastQC v0.10.1 run */
// the file doesn't actually exist, we just need it so the outputDir value can be computed correctly
- private val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")
+ private[flexiprep] val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")
@Test def testOutputDir() = {
val fqc = new Fastqc(null)
@@ -44,7 +44,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
val fqc = new Fastqc(null)
fqc.output = outputv0101
// 11 QC modules
- fqc.qcModules.size shouldBe 11
+ fqc.qcModules.size shouldBe 12
// first module
fqc.qcModules.keySet should contain("Basic Statistics")
// mid (6th module)
@@ -83,4 +83,23 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
adapters.last.seq shouldEqual "GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
}
+
+ @Test def testPerBaseSequenceQuality() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+
+ val perBaseSequenceQuality = fqc.perBaseSequenceQuality
+ perBaseSequenceQuality.size shouldBe 55
+ perBaseSequenceQuality.keys should contain("54-55")
+ }
+
+ @Test def testPerBaseSequenceContent() = {
+ val fqc = new Fastqc(null)
+ fqc.output = outputv0101
+
+ val perBaseSequenceContent: Map[String, Map[String, Double]] = fqc.perBaseSequenceContent
+ perBaseSequenceContent.size shouldBe 55
+ perBaseSequenceContent.keys should contain("1")
+ }
+
}
\ No newline at end of file