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