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# LGTC Bioinformatics
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This will (hopefully) expand, but for now we maintain a list of running projects.
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Martijn:
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||GoNL||Martijn||Full-genome sequencing of 769 Dutch individuals (not really LGTC)||`/data/DIV5/GoNL`||
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||CGD||Martijn||Full-genome sequencing of 9 individuals, Illumina||`/data/LGTC/LGTCusers/mvermaat1/CGD`||
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||Project J||Martijn||Full-genome sequencing of Johan den Dunnen, Illumina||`/data/LGTC/LGTCusers/mvermaat1/johan`||
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||Project K||Martijn||Full-genome sequencing of Marjolein Kriek, Illumina (older data available elsewhere)||`/data/LGTC/LGTCusers/mvermaat1/K`||
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||Project DJ||Martijn||Full-genome sequencing of some DJ (main analysis done by Gijs Santen)||`/data/LGTC/LGTCusers/mvermaat1/projectDJmerged.tmp`||
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||Project D||Martijn||Full-genome sequencing of Nicole Datson (main analysis done by Gijs Santen)||`/data/LGTC/LGTCusers/mvermaat1/projectDmerged2.tmp`||
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||Geuvadis k-mers||Martijn||kMer profiling of Geuvadis data (helping Irina)||`/data/LGTC/LGTCusers/mvermaat1/k-mer/geuvadis`||
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Jeroen:
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|| Location || Status || Description ||
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|| /data/LGTC/LGTCusers/jfjlaros/irina || purged || RNASeq example pipeline ||
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|| /data/LGTC/LGTCusers/jfjlaros/isabella || purged || RNASeq / demultiplexing ||
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|| /data/LGTC/LGTCusers/jfjlaros/pastink || purged || ||
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|| /data/LGTC/LGTCusers/jfjlaros/twin || purged || Variant calling IonTorrent ||
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|| /data/LGTC/LGTCusers/jfjlaros/yu/42V9B_s_6 || purged || Large deletions test ||
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|| /data/LGTC/LGTCusers/jfjlaros/yu/42V9B_s_7_8 || purged || VCF disambiguation test ||
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|| /data/LGTC/LGTCusers/jfjlaros/yu/42VGT_s_7 || purged || Demultiplexing ||
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|| /data/LGTC/LGTCusers/jfjlaros/yu/42VGT_s_7_make || purged || Large deletions. ||
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|| /data/LGTC/LGTCusers/jfjlaros/elze || purged || Demultiplexing ||
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|| /data/LGTC/LGTCusers/jfjlaros/galaxyExome || saved || Test files for galaxy ||
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|| /data/LGTC/LGTCusers/jfjlaros/johan/exons || busy || Mononucleotide stretches in exons ||
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|| /data/LGTC/LGTCusers/jfjlaros/johan/repeats || busy || Mapping of repeating sequences. ||
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|| /data/LGTC/LGTCusers/jfjlaros/galaxy || saved || Backup of Matt's galaxy work ||
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|| /data/LGTC/LGTCusers/jfjlaros/artificial_set || saved || Fake Y-chromosome for benchmarking ||
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|| /data/LGTC/LGTCusers/jfjlaros/pietro || purged || mm9 DMD RNASeq ||
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|| /data/LGTC/LGTCusers/jfjlaros/tahar || purged || Amplicon ||
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|| /data/LGTC/LGTCusers/jfjlaros/kasper || purged || L.dominicanus amplicon ||
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|| /data/LGTC/LGTCusers/jfjlaros/ken || purged || Fish owl k-mer ||
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|| /data/LGTC/LGTCusers/jfjlaros/trisomy || purged || Non-invasive trisomy detection ||
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|| /data/LGTC/LGTCusers/jfjlaros/1000Genomes || saved || Variant calling reference data ||
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|| /data/LGTC/LGTCusers/jfjlaros/mariella || purged || Exome ||
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|| /data/LGTC/LGTCusers/jfjlaros/proton || busy || Full genome IonProton ||
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|| /data/LGTC/LGTCusers/jfjlaros/lenie || busy || Acinetobacter plasmid assembly ||
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|| /data/LGTC/LGTCusers/jfjlaros/boukje/old || purged || Exome ||
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|| /data/LGTC/LGTCusers/jfjlaros/boukje/BV2 || purged || Exome ||
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|| /data/LGTC/LGTCusers/jfjlaros/henk/cdna || busy || CDNA synthesis ||
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|| /data/LGTC/LGTCusers/jfjlaros/henk/depletion || purged || Transcript depletion ||
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|| /data/LGTC/LGTCusers/jfjlaros/henk/normalisation || busy || Transcript normalisation ||
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|| /data/LGTC/LGTCusers/jfjlaros/henk/rnaseq || busy || dm3 RNASeq ||
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|| /data/LGTC/LGTCusers/jfjlaros/henk/lenti || busy || Targeted coverage (insertion site). ||
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|| /data/LGTC/LGTCusers/jfjlaros/chrM.k || purged || k-mer complexity ||
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|| /data/LGTC/LGTCusers/jfjlaros/rvdoorn || purged || cancer RNASeq ||
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|| /data/LGTC/LGTCusers/jfjlaros/duplicates || purged || duplicate read in different experiments ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/NMD1 || purged || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/NMD2 || purged || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/NMD3 || purged || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/OPDM || busy || Repeats ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/Seckel || purged || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/gijs/projectD || busy || Comparison genome/exome. ||
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|| /data/LGTC/LGTCusers/jfjlaros/yavuz || busy || Single cell sampleprep ||
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|| /data/LGTC/LGTCusers/jfjlaros/peter || busy || RNASeq ||
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|| /data/LGTC/LGTCusers/jfjlaros/rowida/61WPD_s_7 || purged || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/rowida/D08N1ACXX_s_7 || purged || Pooled exome ||
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|| /data/LGTC/LGTCusers/jfjlaros/GoNL/flagstat || purged || QC plots ||
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|| /data/LGTC/LGTCusers/jfjlaros/GoNL/deltest || busy || Large deletions ||
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|| /data/LGTC/LGTCusers/jfjlaros/willeke || purged || Strand specific RNASeq ||
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|| /data/LGTC/LGTCusers/jfjlaros/sunita/PG1 || purged || E.coli plasmid/genes fingerprinting ||
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|| /data/LGTC/LGTCusers/jfjlaros/sunita/pilot || purged || E.coli plasmid/genes fingerprinting ||
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|| /data/LGTC/LGTCusers/jfjlaros/sunita/ecoli2 || busy || E.coli plasmid/genes fingerprinting ||
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Michiel:
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/C.elegans|| C.e. miSeq test. ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/chrY || Test set for GAPSS. ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/cnv || CNV pipeline . ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/ecoli || Ecoli random barcoding. ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/G3-bedvcf|| Backup of early GAPPS output. ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/kmer-qc || Includes CGD, HR, Exomes. ||
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|| /data/LGTC/LGTCusers/mvangalen/LGTC_rnd/MiSeq || Human miSeq test. ||
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|| /data/LGTC/LGTCusers/mvangalen/projects/dina || Exome data. ||
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|| /data/LGTC/LGTCusers/mvangalen/projects/hDMD || DMD mouse. ||
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|| /data/LGTC/LGTCusers/mvangalen/projects/jwijnen || Exome data. ||
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|| /data/LGTC/LGTCusers/mvangalen/projects/lenie || Microbe and plasmid data. ||
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jfrank:
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||**Nickname**||**Description**||**Status**||**Location**||
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||SolV||SMRT *de novo* genome assembly and its evaluation.[collaboration with the microbiology department of[[BR]([BR]]In)]Radboud University Nijmegen and Ken Kraaijeveld.||Nearly finished||`~LGTCusers/jfrank/SolV`||
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||Helicobacter||SMRT *de novo* genome assembly.[[BR]]Celia van der Spek, Els Robanus Maandag, LUMC, HG.||Finished||`~LGTCusers/jfrank/z_Other/Helicobacter`||
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||Celera Assembler||Running pacBioToCA and Celera Assembler on the Shark SGE grid.||Finished||[https://humgenprojects.lumc.nl/trac/shark/wiki/pacBioToCA]||
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||Clavipes||*Leptopilina clavipes* & its *Wolbachia* endosymbiont[*de novo* genome assembly. In collaboration with[[BR]([BR]]Hybrid)]UMC Groningen and Ken Kraaijeveld.||Nearly finished||`~/LGTCusers/jfrank/Clavipes`|| |