Only use a random subset of genes for generating core aln #260
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…sters passed the core frequency threshold
Added a `--core_subset` argument to every command with which a user can choose to generate a core genome alignment. When using large datasets the core genome alignment takes a substantial amount of time, but perhaps a reasonable sample would produce the same phylogenetic signal in a fraction of the time
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Thanks very much for this! I've just got back from holiday and am planning to work on Panaroo this week so will try and incorporate this option into the next release. We've also been working on identifying gene families that are more reliable for inferring phylogenies. At the moment we've incorporated an entropy based approach. The filtered alignments are currently output as |
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Added a
--core_subsetargument to every command with which a user can choose to generate a core genome alignment.When using large datasets the core genome alignment takes a substantial amount of time, but perhaps a reasonable sample would produce the same phylogenetic signal in a fraction of the time
Tested briefly on a toy dataset, opening a PR in case this is a useful new argument!