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snippy-core (version 4.6.0+galaxy0)
Select all the snippy inputs for alignment
Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.
Select genome from the list

snippy-core @VERSION@

Combine multiple Snippy outputs into a core SNP alignment

If you call SNPs for multiple isolates from the same reference, you can produce an alignment of "core SNPs" which can be used to build a high-resolution phylogeny (ignoring possible recombination). A "core site" is a genomic position that is present in all the samples. A core site can have the same nucleotide in every sample ("monomorphic") or some samples can be different ("polymorphic" or "variant"). If we ignore the complications of "ins", "del" variant types, and just use variant sites, these are the "core SNP genome".


Multiple Snippy output directories. (At least 2 of)


  • noreference Exclude reference (default '0').


snippy must have been run with --cleanup False