Available pipelines:

 

GenAP_Pipes are under continuous development. Below is a list of your current pipelines.
 
 

Experiment pipeline Flag more Info
ChIP-Seq chipseq.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/chipseq/
RNA-Seq rnaseq.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/rnaseq/
De novo RNA-Seq rnaseq_denovo_assembly.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/rnaseq_denovo_assembly/
Whole Genome Seq dnaseq.py default https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/dnaseq/
Exome Seq dnaseq.py capture bed file in Readset file or ini file https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/dnaseq/
Deep Whole Genome Seq dnaseq_high_coverage.py default https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/dnaseq_high_coverage/
Deep Exome Seq dnaseq_high_coverage.py capture bed file in Readset file or ini file https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/dnaseq_high_coverage/
Hi-C hicseq.py -t hic https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/hicseq/
Capture Hi-C hicseq.py -t capture https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/hicseq/
Whole Genome Methyl Seq methylseq.py default https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/methylseq/
Capture Methyl Seq methylseq.py capture bed file in Readset file or ini file https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/methylseq/
Cancer Analysis tumor_pair.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/tumor_pair/
Meta Genomics ampliconseq.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/ampliconseq/
PacBio Assembly pacbio_assembly.py https://bitbucket.org/mugqic/mugqic_pipelines/src/master/pipelines/pacbio_assembly/

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