🐍 Snakemake wrappers for bioinformatics.
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.circleci Write tests for feature-counts. Sep 8, 2018
bismark Update wrapper environment specification. Sep 4, 2018
bsmap Update wrapper environment specification. Sep 4, 2018
bwa-meth Update wrapper environment specification. Sep 4, 2018
bwa Update wrapper environment specification. Sep 4, 2018
cufflinks Fix typo in cufflinks rule. Sep 6, 2018
deg Update wrapper environment specification. Sep 4, 2018
fastp Update wrapper environment specification. Sep 4, 2018
fastqc Update wrapper environment specification. Sep 4, 2018
feature-counts Write tests for feature-counts. Sep 8, 2018
freebayes Fix typo in freebayes rule. Sep 20, 2018
hisat2 Update wrapper environment specification. Sep 4, 2018
htseq/count Update wrapper environment specification. Sep 4, 2018
kallisto Fix bugs in kallisto environment. Sep 8, 2018
parallel-fastq-dump Update wrapper environment specification. Sep 4, 2018
rsem Update wrapper environment specification. Sep 4, 2018
salmon Write salmon rules. Sep 14, 2018
sambamba Refactor wrappers. Sep 4, 2018
samtools Write tests for samtools. Sep 4, 2018
snpeff/ann Write tests for snpeff/ann. Sep 8, 2018
sra-tools/prefetch/accession Write prefetch/accession rule. Sep 4, 2018
star Fix typo in star/2-pass rule. Sep 14, 2018
strelka/tumor-normal Fix strelka rules. Sep 18, 2018
subsample-fastq Fix subsample-fastq test suite. Sep 5, 2018
trim-galore Write test for trim-galore with single-reads. Sep 4, 2018
wgsim Write tests for wgsim. Sep 5, 2018
.gitignore Add .gitignore. Jul 26, 2018
README.md Add snakemake badge in README.md. Sep 6, 2018

README.md

snakemake-wrappers

Snakemake wrappers for bioinformatics.

Available wrappers

Routine analysis

  • DEG discovery
    • DESeq2
    • EBSeq
    • edgeR

Variant calling

  • freebayes

File format handlers

  • sambamba
    • index
    • sort
    • markdup
  • samtools
    • index
    • sort

Data retrieval

  • sra-tools
    • prefetch
      • accession
  • parallel-fastq-dump

Preprocessing

  • fastqc
  • trim-galore
  • fastp

Aligner

  • bismark
    • genome-preparation
  • bsmap

Gene expression quantification

  • rsem
    • calculate-expression
      • pe
    • prepare-reference
  • kallisto
    • index
    • quant
  • salmon
    • index
    • quant

Misc

  • subsample-fastq