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transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
GNU General Public License v3.0
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update #80

Closed yjiakang closed 1 year ago

yjiakang commented 1 year ago

Thanks for your awesome pipeline. I saw that the last update of your pipeline was by 2021. Is it suitalbe for data today also?

transcript commented 1 year ago

Hi yjiakang,

You can still use this pipeline today, yes, although I'll note that the functional categorization SEED Subsystems database has not been updated since the mid-2010s and is growing increasingly outdated. The RefSeq annotations are all still valid and up-to-date.

If you're looking for an alternative, you could also check out HUMAnN2, which gets a bit more love than this pipeline.