AstrobioMike/bit: v2.10.0

Added

• bit dl-ncbi-assemblies can now be passed -t | --target-taxon instead of, or in addition to, accessions to the -w parameter
  • run bit dl-ncbi-assemblies -H to see the detailed help menu which includes a slew of new parameters
    • like controlling which source db, reps only, which section of ncbi, min/max completeness filters, assembly-level filters
  • this finally replaces needing to run get-accs-from-gtdb/ncbi and then passing them to the dl program

Changed

• bit get-accs-from-ncbi
  • the previous --source parameter has been changed to --ncbi-section to leave source to be consistent with other things in bit
• --derep-rank on bit get-accs-from-gtdb and bit get-accs-from-ncbi now defaults to auto instead of off, matching bit dl-ncbi-assemblies
  • this changes default output — a plain bit get-accs-from-* -t <taxon> now returns a dereplicated set. Pass --derep-rank off for the old behavior
  • --derep-rank auto (the default) is two ranks finer than the target (one rank finer for eukaryotes), one step finer if target is a genus, and becomes off when the target is a species (explictly set --derep-rank species if you really want just one member of a species)
• --ncbi-section on bit get-accs-from-ncbi now defaults to both rather than refseq, also matching bit dl-ncbi-assemblies
  • the refseq default had been standing in for redundancy removal, which --derep-rank auto now handles directly, while also ensuring maximum breadth of diversity is maintained

Fixed

• output metadata table from bit get-accs-from-gtdb could sometimes be mangled at the top, fixed now

Full Changelog: https://github.com/AstrobioMike/bit/compare/v2.9.2...v2.10.0