RNAseq multi method

Requirements

• A (mini-)conda installation
• A snakemake installation
• pandas (python3 library)
• cerberus (python3 library)
• biopet tools:
  • bamstats
  • basecounter
  • extractadaptersfastqc
• GATK (3.8)
• Picard

Included Mappers

• STAR
• STAR 2-pass
• HISAT2

Included Counting methods

• HTSeq-count
• featureCounts
• STAR QuantMode
• basecounter
  • exon
  • intron
  • transcript
  • gene
• Salmon (alignment free)

Included variantcallers

• HaplotypeCaller
• Varscan

Other included tools:

• Centrifuge

Author

Davy Cats ([email protected])