Add `sourmash index` option

nf-core / kmermaid

k-mer similarity analysis pipeline

https://nf-co.re/kmermaid

MIT License

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Open olgabot opened 4 years ago

olgabot commented 4 years ago

While I'm not doing a lot of sourmash compare (see https://github.com/nf-core/kmermaid/issues/75) I may still want to make an SBT index.

Reasons:

SBT indices are easy to add a single new sample to, comparison matrices are not
SBT matrices may (eventually..) be localized and fed into KNN graph algorithm using tools like UMAP (https://github.com/dib-lab/sourmash/pull/925)

pranathivemuri commented 4 years ago

for this issue, is sourmash index done on all the sketches from peptides, nucleotides, and ska sketch results?