Snippy

note

Rapid haploid variant calling and core genome alignment.

https://github.com/tseemann/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