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[MRG] add script for merging signatures by value in spreadsheet column #1

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merged 5 commits into from
Apr 6, 2022

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bluegenes
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@bluegenes bluegenes commented Apr 6, 2022

For example, to merge into a single signature per species:

python mass-merge.py -F gtdb-rs202.taxonomy.v2.csv gtdb-rs202.nucleotide-k31.zip \
-o gtdb-rs202.nucleotide-k31.species.zip --merge-col species

motivation:

for gtdb rs202 db

  • ~70% of database belongs to species with >=10 genomes represented
  • ~ 50% belongs to species w/ >=100 genomes represented.
    A merged db should save significant space by eliminating redundancy in hashes shared across strains and be good enough for many non-strain analyses.

7.7G full db --> 1.6G species database (k 31, scaled 1000)

@bluegenes bluegenes merged commit 498d6ac into main Apr 6, 2022
@bluegenes bluegenes deleted the add-mass-merge branch April 6, 2022 20:59
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2 participants