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Snippy

Supported Tool

Rapid haploid variant calling and core genome alignment.

Description

The Snippy module parses output generated by snippy. The following commands are implemented:

  • snippy
    • Variant type descriptive statistics.
    • Parses summary prefix.txt file that is generated.
  • snippy-core
    • Core genome alignment descriptive statistics.
    • Parses summary prefix.txt file that is generated.

File search patterns

snippy/snippy:
  contents: snippy
  num_lines: 20
snippy/snippy-core:
  contents_re: ID\tLENGTH\tALIGNED\tUNALIGNED\tVARIANT\tHET\tMASKED\tLOWCOV
  num_lines: 1