Core-SNP alignment from Snippy outputs
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
Annotated variants in VCF format
*.vcf.gz
aligned_fa{:bash}
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{:bash}
Reference genome in GenBank (preferred) or FASTA format
*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}
aln{:bash}
${prefix}.aln{:bash}
A core SNP alignment in FASTA format
*.aln
full_aln{:bash}
${prefix}.full.aln{:bash}
A whole genome SNP alignment (includes invariant sites)
*.full.aln
tab{:bash}
${prefix}.tab{:bash}
Tab-separated columnar list of core SNP sites with alleles but NO annotations
*.tab
${prefix}.vcf{:bash}
Multi-sample VCF file with genotype GT tags for all discovered alleles
*.vcf
txt{:bash}
${prefix}.txt{:bash}
Tab-separated columnar list of alignment/core-size statistics
*.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Rapid bacterial SNP calling and core genome alignments
