v1.0.1

This is the first v1.0 patch release (v1.0.1) fixing some bugs & typos and add a couple of minor improvements.

Compatible database scheme version: v2.0

Bug fixes:

• fix calculation of GC & N50 stats: 2829a24 (Thanks Matthew Croxen)
• fix a typo in GenBank/EMBL output: 1595133 (Thanks @davised)

Improvements:

• download/update AMRFinderPlus db upon Bakta db download/update: 94ccc69
• add a short note to error msg if AMRFinderPlus db is not available: 750396f
• add more sORF unit tests: 685a3bc
• fix link to old db files: 140e348 (Thanks @davised)
• readme updates & improvements

v1.0 - In all beginnings dwells a magic force

This is the first official and stable v1.0 release introducing many new features and countless bug fixes.

Compatible database scheme version: 2 v2.0

New features and improvements over 0.5:

• expert annotation systems comprising AMRFinderPlus, BlastRules and VFDB
• support for EMBL flat files; INSDC-compliant and submission-ready, validated via ENA Webin-CLI
• db download from within Bakta: bakta_db --help
• parallelized sORF overlap filter significantly reduces wall clock runtimes
• replicon files can also be provided as CSV
• more integration tests added
• code reviews & optimizations
• updated readme and usage

as well as countless bug fixes.

v1.0-rc3

This is the 3rd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Bug fixes over rc2:

• several INSDC qualifier issues (1d0f6dc 1d0f6dc)
• INSDC tRNA anticodon and pseudo qualifier issues (ff668d5 fb03559)
• lacking python __init__ file (0560102)

Plus several minor bug fixes & improvements.

v1.0-rc2

This is the 2nd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Improvements over rc1:

• added parameter argument checks
• added more tests
• updated usage and readme

Bug fixes:

• fixed name of main entry module

v1.0-rc1

This is a v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Further improvements:

• db download logic
• parallelized sORF overlap filter
• support for EMBL flat file output
• replicon files can also be provided as csv
• more integration tests added
• several code reviews & optimizations

Bug fixes:

• fix max sORF length to 29

v0.5 - Hypotheticals: rule them all(most)

Improvements:

• analysis & output of hypothetical proteins added (pfam detection & calculation of sequence statistics)
• improved CI
• improved DB compilation process
• added annotation summary to GenBank output files
• added CWL file

Bug fixes:

• fix error msgs

v0.4 - Let there be tests...

Improvements:

• automated integration tests added
• genome & plasmid test sequences added
• massively improved fasta output performance
• several genbank flat file output improvements
• code reviews
• adhere to translation table in sORF detection

Bug fixes:

• fix annotations of truncated CDS
• fix truncated CDS positions in GenBank

v0.3.2

Fix breaking bug in annotation statistics.

Patching the first bugs

This is a patch release comprising the following fixes:

• fix Prodigal training file logic (creation & usage)
• fix coding density calculation on edge features

as well as some minor improvements:

• introduce omit_readlock PRAGMA for SQLite queries
• add genome completeness info to JSON output

Initial Release

The first public release for broad testing & debugging.