PathSeq Pre-built DB Breakdown Per Microbial Group

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Renald James Legaspi

• July 06, 2023 01:38

Hi Gatk Devs! I am trying to know the number of members per microbial group (e.g., bacteria, virus...) in the pre-built db in this link gs://gatk-best-practices/pathseq/resources/ I've tried reading/parsing the microbe dB file but wasn't successful converting to a human readable format/data table. Is this information (breakdown) available anywhere? If no, can you suggest ways on reading the microbe dB file to a data table instead. Thank you!

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  Mark Walker

  • July 10, 2023 21:00

  Hello Renald James Legaspi,

  You could infer that from the list of microbes here:

  gs://gatk-best-practices/pathseq/resources/pathseq_microbe_list.txt

  You can use this along with the taxdump file to reconstruct the tree and count up the number of organisms at each taxonomic level:

  gs://gatk-best-practices/pathseq/resources/taxdump.tar.gz

  More on the taxdump file format can be found here:

  https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_readme.txt

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