BIOM output from sample-tally & harmonise ASV naming in output files

peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool

https://thapbi-pict.readthedocs.io/

MIT License

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BIOM output from sample-tally & harmonise ASV naming in output files #608

Closed peterjc closed 7 months ago

peterjc commented 7 months ago

This adds optional BIOM output from the sample-tally step (pre-classifier).

Also, previously our output files used:

TSV: <marker>/<md5>_<abundance>
BIOM: <marker>/<md5>
FASTA: <md5>_<abundance>

Now they all use <marker>/<md5>_<abundance> which is consistent and essential for input to Qiime2 (which currently needs the FASTA separately from the "feature table" part of the BIOM file).