v2.7.0

Added

• to bit gen-metagenome
  • taxid and detection columns in the per-genome truth tsvs
• to bit gen-reads
  • per-genome output tsv with info like number of reads generated, coverage, and detection

Full Changelog: v2.6.0...v2.7.0

v2.6.0

Added

• bit gen-metagenome
  • leverages bit get-accs-from-gtdb, bit dl-ncbi-assemblies, bit mutate-seqs, bit gen-reads, and bit lineage from-taxids to produce mock metagenomes with ground-truth tables per-genome, per-taxonomic-rank, and per-read with associated GTDB and NCBI taxonomy
• bit get-accs-from-ncbi for searching ncbi for assembly accessions based on taxonomy (corollary to bit get-accs-from-gtdb)
• bit gen-reads
  • has an optional --source-tsv option which will write out each read's source info (and when set, the headers no long hold all that info and are smaller)
  • can now take gzipped input fastas
• added a github action to weekly rebuild the slimmed down ncbi assembly summary table

Changed

• bit dl-ncbi-assemblies
  • many robustification improvements
  • output fasta files have extension ".fasta.gz" now instead of ".fa.gz" for consistency with the rest of bit-produced nt fasta files (sorry for the change!)
• bit gen-reads
  • read headers have been improved with regard to provenance tracking
  • initial fragments/reads now have a 50/50 chance to be drawn from +/- strand (relative to the ref)
• bit data get gtdb-data and bit data get ncbi-assembly-data now both pull a prepared, slimmed version from github first if possible (saves on download and reading time)

Full Changelog: v2.5.0...v2.6.0

NCBI assembly-info (latest)

an auto-weekly-rebuilt slimmed down NCBI assembly summary table that bit uses

GTDB metadata (latest)

an auto-maintained slimmed down GTDB metadata table that bit uses (it's stored date file is checked weekly, and this is rebuilt when it sees that GTDB has issued a new release)

Metagenomics workflow v1.0.4

• removed f-strings and made shell blocks raw/r so Snakefile was compatible with bit env python 3.12

Amplicon workflow v1.0.1

• removed unnecessary f-strings to work with updated bit env python 3.12

v2.5.0

Base env python updated from 3.10 to 3.12

Added

• to bit ez-screen assembly
  • region-calls.tsv now includes a contig_length column
• to bit fasta extract-seqs-by-coords
  • can now take an inline entry for a single region to extract instead of requiring a bed file, e.g. -b contig-1 20 100

Changed

• bit fasta extract-seqs-by-headers
  • now ignores ">" characters if they are at the front of the specified headers
  • space-delimited list or file with one header per line can be provided to the -H parameter now

SRA download workflow v1.1.2

• slight changes to some f-strings so it works with python 3.12 (after bit base env migration from 3.10)

v2.4.1

Added

• additions to bit ez-screen assembly
  • --min-edge-perc-cov and --edge-tolerance which enable lower-coverage targets to be captured and reported that are likely to be clipped by the contig edge

v2.4.0

Added

• additions to bit ez-screen assembly
  • can now take multiple nucleotide (as fasta or blast db) and/or amino-acid (as fasta or diamond db) inputs for targets
  • now by default extracts "islands" of densely clustered regions into their own fastas (disable with --no-island-extraction)
  • detailed help menu accessible with -H|--show-detailed-help