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

aln

meta:map

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

]

${prefix}.aln:file

A core SNP alignment in FASTA format

*.aln

full_aln

meta:map

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

]

${prefix}.full.aln:file

A whole genome SNP alignment (includes invariant sites)

*.full.aln

tab

meta:map

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

]

${prefix}.tab:file

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

*.tab

vcf

meta:map

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

]

${prefix}.vcf:file

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

*.vcf

txt

meta:map

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

]

${prefix}.txt:file

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

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

snippy
GPL v2

Rapid bacterial SNP calling and core genome alignments