Added

• [breaking] Add decoy protein sequences (RefSeq fungi, protozoa, viral, plant, and human GRCh38/hg38) which effectively trap non-prokaryotic reads and prevent them from inflating total prokaryotic genome copy estimates if the pre-filtering module (default with Kraken2) is not enabled. Pre-filtering is no longer necessary even if samples are contaminated with human DNA or other common eukaryotes/viruses, unless the mean genome size of prokaryotes needs to be estimated. See 8918168 for more details. This function requires a database released on or after 2024-06-28.

Changed

• Simplify filtering criteria for alignments.

Changed

• Prevent extract_sequence from loading all marker-containing reads into memory.
• Change -F to --frameshift and max_iteration to max_iterations for consistency.
• Switch from figshare to zenodo for better database versioning.

Fixed

• Fix a bug causing tqdm being disabled (3bbd087).

Changed

• Use tqdm for logging.
• Reduce peak memory usage by parsing PAF files on the fly.

Changed

• Change alignment filtering criteria: make AS cutoff more stringent, drop MS. See 7cc6dbd for details.

Fixed

• Fix a bug causing total genome copies not being properly calculated with diamond>=2.1.9.

Added

• Output both gap-compressed and gap-uncompressed (BLAST-like) identity.
• Refine output format.

Added

• Add gap-compressed ANI to output.

Added

• Add options to control EM early stop.

Changed

• Use scipy.sparse to reduce peak memory usage and computational time.
• Change default terminal condition of EM (max_iteration: 100 -> 1000; epsilon: 1e-5 -> 1e-10).

Fixed

• Fix a bug causing chimeric reads not being aggregated.

Added

• Output a json file to indicate the lineage of processed reads.

Changed

• Make databases indexed by default.
• Use only kraken's prediction for removal of non-prokaryotic reads.
• Change --db_kraken to --db-kraken for consistency.
• Change sp[0-9]+ to sp[0-9]+ for consistency.
• Change copies to copy in output files for consistency.

Fixed

• Prevent numpy from using all logical cores.

Added

• First release.