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Bismark

Supported Tool

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

Description

The Bismark module parses logs generated by Bismark, a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

File search patterns

bismark/align:
  fn: "*_[SP]E_report.txt"
bismark/dedup:
  fn: "*.deduplication_report.txt"
bismark/meth_extract:
  fn: "*_splitting_report.txt"
bismark/m_bias:
  fn: "*M-bias.txt"
bismark/bam2nuc:
  fn: "*.nucleotide_stats.txt"