filter: Expand subsampling docs #1425
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victorlin
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Feb 24, 2024
huddlej
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These docs have been needed for so long, so thank you for making them a reality, @victorlin. With the exception of some minor typos that @jameshadfield pointed out, you could easily merge this now and it would be a big help to users. I made a few comments below that mostly attempt to clarify the content for new users.
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As a thought experiment, it would be interesting to see how we'd implement these same |
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I've resolved all conversations above. Will merge on any approval. |
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joverlee521
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Feb 27, 2024
- Use section headings. - Remove references to zika-tutorial. It's largely independent of that and prone to getting out of sync. - Use --output-sequences and --output-metadata. - Fix indentation.
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This was referenced Mar 6, 2024
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(preview)
Description of proposed changes
Expand subsampling docs with a guide on how to implement multi-pass subsampling¹.
¹ internal subsampling doc definition of "multi-pass subsampling": Subsampling done as multiple calls to a subsampling tool, where intermediate subsamples are created and joined together to create a final/combined sample. It is used to work around limitations on what can be done in a single pass.
Related issue(s)
Checklist
docs/guides/bioinformatics: Add guide on filtering and subsampling docs.nextstrain.org#192--exclude/--include(ref)