Release notes Biopet version 0.6.0

General Code changes

  • Refactoring Gentrap, It's modules can now be used outside of gentrap also
  • Added more unit testing
  • Upgrade to Queue 3.5
  • MultisampleMapping is now a base for all multisample pipelines with a default alignment step


  • Gears: Metagenomics NGS data. Added support for 16S with Kraken and Qiime
  • Raise an exception at the beginning of each pipeline when not using absolute paths
  • Moved Varscan from Gentrap to Shiva (Varscan can still be used inside Gentrap)
  • Gentrap: now uses shiva for variantcalling and produce multisample vcf files
  • Added Bowtie 2
  • Added fastq validator, flexiprep now aborts when a input file is corrupted
  • Added optional vcf validator step in shiva
  • Added optional Varda step in Toucan
  • Added trimming of reverse complement adapters (flexiprep does this automatic)
  • Added Tinycap for smallRNA analysis
  • Gentrap: Refactoring changed the "expression_measures" options
  • Fixed biopet logging
  • Added sample tagging
  • Seqstat now reports histogram of read lengths
  • Fixed bug in seqstat when having multiple sizes exists in the fastq file
  • Added variant plots for targets to report of Shiva
  • Adapter feed to cutadapt now use only that parts that are reported by fastqc and not the full sequence
  • Added a reference selector when fasta file can't be found. User now get a list of available species and genomes in the config
  • Fixed bcftools with IUPAC symbols

Infrastructure changes

  • Development environment within the LUMC is now tested with Jenkins
    • Added integration tests for Gentrap
    • Added integration tests for Gears
    • Added general MultisampleMapping testing