v1.3.20

• Update extraction of gene cluster GenBank files from full GenBank files in fai to be much more efficient in fai. Time difference mostly noticeable for metagenomic application where full GenBank files can be quite large.

Update to v1.3.19

Major Updates:

• Slight update to core ortholog group determining algorithm in zol to reduce memory consumption and aid scalability without a dereplicaiton/re-inflation approach.
• Slight update to processing of miniprot protein mappings to account for overlap in exon coordinates (best scoring exon is selected in such cases) in prepTG.
• New mode in zol where users can provide known instances of a gene cluster and determine appropriate parameters for searching for additional instances using fai.

Minor Updates:

• New script to extract proteins from GenBank files into FASTA format, extractProteinsFromGenBank.py.

v1.3.18

• Add option to prepTG to easily/automatically create databases for any bacterial genus/species in GTDB.

What's Changed

• Update prepTG by @raufs in #62
• Update prepTG by @raufs in #63
• Raufs patch 3 by @raufs in #64

Full Changelog: v1.3.17...v1.3.18

v1.3.17

• Update fai catching of cases when no homologous BGC instance is found among target genomes.
• Round metrics in fai's report.
• Temporarily remove abon, atpoc, apos from Docker wrapper as these are not yet working in Docker (only available via bioconda) - will aim to have them working via Docker image in the near future!

What's Changed

• Update README.md by @raufs in #61

Full Changelog: v1.3.16...v1.3.17

v1.3.16

• Correct mis-match between default E-value cutoff (1e-10) for simple BLASTp mode in abon, apos, and atpoc in help function and actual default value (1e-5). Default cutoff has been 1e-5 since the introduction of the simple BLASTp mode.

What's Changed

• Update README.md by @raufs in #58
• Update README.md by @raufs in #59
• Update/match-up default E-value cutoff in simple BLAST options for abon, apos, and atpoc by @raufs in #60

Full Changelog: v1.3.15...v1.3.16

v1.3.15

• Add missing -p meta for usage of prodigal-gv

v1.3.12

• Introduce apos (assess plasmid-ome similarity) and atpoc (assess temperate phage-ome conservation) to assess conservation of a focal sample's plasmids and phages across some set of target/database genomes (e.g. all other genomes in the same species/genus as the sample)
• Add prodigal-gv option in prepTG and fai.
• Add simple BLASTp search option in place of fai for abon.

What's Changed

• Update README.md by @raufs in #52
• Update atpoc by @raufs in #53

Full Changelog: v1.3.11...v1.3.12

v1.3.11

• Introduce abon!
• Update links to newer versions of precompiled prepTG databases for select bacterial taxa.
• Update wiki documentation.

What's Changed

• Update test_docker.sh by @raufs in #50
• Update abon by @raufs in #51

Full Changelog: v1.3.10...v1.3.11

v1.3.10

• Introduce clean up option in fai.
• Reorganize fai's results directory.
• Generate Tiny AAI figure and an XLSX spreadsheet in fai to allow for manual curation of homologous gene clusters detected.

What's Changed

• Update README.md by @raufs in #48
• Update run_tests.sh by @raufs in #49

Full Changelog: v1.3.9...v1.3.10

v1.3.9

• Correct new logic for more robustly determining consensus order introduced recently in v1.3.7.

What's Changed

• Update README.md by @raufs in #46
• Correct if/else logic when determining consensus order by @raufs in #47

Full Changelog: v1.3.8...v1.3.9