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biopet.biopet
Commits
67d911cd
Commit
67d911cd
authored
Jul 28, 2015
by
Peter van 't Hof
Browse files
Adding minimal config
parent
b0289eef
Changes
1
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docs/pipelines/mapping.md
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67d911cd
...
...
@@ -10,9 +10,12 @@ After the QC, the pipeline simply maps the reads with the chosen aligner. The re
*
[
Flexiprep
](
flexiprep.md
)
*
Alignment programs:
*
<a
href=
"http://bio-bwa.sourceforge.net/bwa.shtml"
target=
"_blank"
>
BWA
</a>
*
<a
href=
"http://bio-bwa.sourceforge.net/bwa.shtml"
target=
"_blank"
>
Bwa mem
</a>
*
<a
href=
"http://bio-bwa.sourceforge.net/bwa.shtml"
target=
"_blank"
>
Bwa aln
</a>
*
<a
href=
"http://bowtie-bio.sourceforge.net/index.shtml"
target=
"_blank"
>
Bowtie version 1.1.1
</a>
*
<a
href=
"http://www.well.ox.ac.uk/project-stampy"
target=
"_blank"
>
Stampy
</a>
*
<a
href=
"http://research-pub.gene.com/gmap/"
target=
"_blank"
>
Gsnap
</a>
*
<a
href=
"https://ccb.jhu.edu/software/tophat"
target=
"_blank"
>
TopHat
</a>
*
<a
href=
"https://github.com/alexdobin/STAR"
target=
"_blank"
>
Star
</a>
*
<a
href=
"https://github.com/alexdobin/STAR"
target=
"_blank"
>
Star-2pass
</a>
*
<a
href=
"http://broadinstitute.github.io/picard/"
target=
"_blank"
>
Picard tool suite
</a>
...
...
@@ -58,6 +61,16 @@ Note that one should first create the appropriate [settings config](../general/c
Any supplied sample config will be ignored.
### Example config
#### Minimal
```
json
{
"reference_fasta"
:
"<path/to/reference"
>
,
"output_dir"
:
"<path/to/output/dir"
>
}
```
#### With options
```
json
{
"reference_fasta"
:
"<path/to/reference"
>
,
...
...
@@ -109,5 +122,6 @@ To perform a dry run simply remove `-run` from the commandline call.
├── <samplename>-lib_1.dedup.bam
├── <samplename>-lib_1.dedup.metrics
├── flexiprep
└── metrics
├── metrics
└── report
~~~
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