Description

Core-SNP alignment from Snippy outputs

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

vcf (file)

Annotated variants in VCF format

*.vcf.gz

aligned_fa (file)

A version of the reference but with - at position with depth=0 and N for 0 < depth < —mincov (does not have variants)

*.aligned.fa.gz

reference (file)

Reference genome in GenBank (preferred) or FASTA format

*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

aln (file)

A core SNP alignment in FASTA format

*.aln

full_aln (file)

A whole genome SNP alignment (includes invariant sites)

*.full.aln

tab (file)

Tab-separated columnar list of core SNP sites with alleles but NO annotations

*.tab

vcf (file)

Multi-sample VCF file with genotype GT tags for all discovered alleles

*.vcf

txt (file)

Tab-separated columnar list of alignment/core-size statistics

*.txt
author
Github user rpetit3
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Tools

snippy
GPL v2

Rapid bacterial SNP calling and core genome alignments

github.com/tseemann/snippy