v1.8.1

This is the first v1.8 patch release (v1.8.1) catching up an overlooked PR.

Improvements:

• Added all valid expert system hits to the final dbxrefs and JSON results: #198 #199 (Thanks @davidtong28)

Important:
#199 introduced a breaking change in the JSON data structure of the feature->expert section. expert was changed from a dictionary (expert system -> hit) to a flat list of expert hits now having a new type field.

v1.8 - May the --force (parameter) be with you

This is the eighth minor release (v1.8) introducing a new output option and various minor improvements.

Compatible database scheme version: 5

Improvements:

• Introduced a new --force option explicitly allowing to overwrite existing data: #200 (Thanks @Dx-wmc)
• Increased sensitivity of protein sequence expert system: #197 (Thanks @davidtong28)
• Improved compatibility of FNA output with NCBI Bankit Submission: #201 (Thanks @menickname)
• Improved --plasmid parameter functionality: #201 426bfd3
• Introduced output of bakta_proteins full annotation results as JSON: #204 (Thanks @Rridley7)
• Refactored QC and description of imported genome sequences: af835b4

Fixes:

• Fixed rare occasions of wrong 5' / 3' ("prime") characters in product descriptions: #215 (Thanks @axbazin)

v1.7 - Lightweight database & harmonized gene symbols

This is the seventh minor release (v1.7) introducing a lightweight database version, various gene symbol improvements, and a metagenome mode.

Compatible database scheme version: 5

New features:

• Introduced a lightweight database version: #196 (Thanks @tseemann))
• Introduced an operon gene symbol harmonization feature: #190
• Introduced a simple metagenome mode: #191
• Added IS transposase to protein expert system: #10

Improvements:

• Improved CDS gene symbols: #186
• Amended tRNA & rRNA gene symbols: #192
• Amended uppercase ncRNA gene symbols: #194
• Added model IDs and dbxrefs to expert annotation systems: #183 (Thanks @davidtong28)
• Updated to Pyrodigal v2.1.0 fixing a bug in the SD motif-detection on reverse contig edges: 599fe70

Fixes:

• Fixed system-wide db path stored in software volume: #177 (Thanks @standage)

v1.6.1

This is the first v1.6 patch release (v1.6.1) fixing 2 bugs.

Improvements:

• Deactivated Circos' max contig limit: 0962df7

Bug fixes:

• Fixed P(y)rodigal meta mode for short sequences and provided training files: #175 (Thanks @pimarin)
• Fixed an unbound variable in bakta_plot: #174 (Thanks @Rridley7)

v1.6 - Draw me a genome, using P(y)rodigal

This is the sixth minor release (v1.6) introducing the creation of circular genome/plasmid plots and fixing false de novo gene predictions by Prodigal.

Compatible database scheme version: 4

New features:

• Creation of circular genome/plasmid plots using Circos: #163 #166

Improvements:

• Replace Prodigal by pyrodigal fixing false gene prediction scores on reverse strands: #149 #165 (Thanks @jhahnfeld, @althonos)
• Improve tRNA product descriptions including anticodons: #170 #173 (Thanks @acvill)

Fixes:

• Fix issues with IUPAC ambiguity codes on tRNA prediction using tRNAscan-SE: #150

v1.5.1

This is the first v1.5 patch release (v1.5.1) fixing a crucial bug causing Diamond runtime errors during the pseudogene detection step. A patch upgrade is highly recommended!

Improvements:

• Added a --debug option in order to keep temporary files for debugging purposes: #137 #141 (Thanks @EricDeveaud)
• Bakta now obeys the number of available CPUs instead of mere CPU counts on Linux: #135 #139 (Thanks @EricDeveaud)
• The Docker image now allows the direct execution of Bakta via Singularity's exec mode in Nextflow: #138 #144 (Thanks @rujinlong & @lukasjelonek)

Bug fixes:

• Fixed an IndexError during the pseudogene detection: #130 #133 (Thanks @samnooij & @jhahnfeld)
• Fixed an off-by-1 error: #131 (Thanks @jhahnfeld)

v1.5 - Pseudogenes, they're coming...

This is the fifth minor release (v1.5) introducing the detection of pseudogenes and KEGG Kofams, along with several improvements.

Compatible database scheme version: 4

New features:

• detection of CDS pseudogenes: #4 (Thanks @jhahnfeld)
• pre-annotation of PSCs with KEGG's Kofams also massively increasing the number of available E.C. numbers: #9

Improvements:

• pre-annotation of PSCs with NCBI's NCBIfams leading to many improved functional annotations: e268df2 #102 (Thanks @hkaspersen)
• add CI tests for species / strain parameters: a98670b
• revert oriCVT inference tags in compliant mode: 4f31ab4
• improve the functional pre-annotation: 46e645a de55d30 1893220 1835574

v1.4.2

This is the second v1.4 patch release (v1.4.2) fixing wrong EC annotations in compliant mode.

Improvements:

• added GFF3 inference tags in compliant mode for ncRNA region, CRISPR, oriC, oriV, oriT: 85c9c42 d81d9b7 a5b31af
• improved chromosome/plasmid auto detection: 9a83055
• refactored code: 606c237 21e6470 b36172c

Bug fixes:

• fixed EC_number annotation in compliant mode: 2960e6b

v1.4.1

This is the first v1.4 patch release (v1.4.1) fixing a tiny simple but critical bug causing all imported contigs being treated as complete sequences. A patch upgrade is highly recommended!

Improvements:

• removed trailing asterik chars on AA import #97: a447f32
• caught AA bulk annotation import errors #97: 58cedf1

Bug fixes:

• fixed fasta import contig attribute types #108
• fixed dnaA/repA revisions #108 (Thanks @conmeehan)

v1.4 - Some exceptional translations

This is the fourth minor release (v1.4) introducing the detection of translational exceptions and protein bulk annotations.

Compatible database scheme version: 3

New features:

• detection & annotation of selenocysteine translational exceptions: #100
• support for protein bulk annotations (direct annotation of proteins w/o genomes): #101 (Thanks @conmeehan)

Improvements:

• maintainability improvements like Python type hints code refactorings: #96 943485c
• added a large(r) genome test dataset and a corresponding Nextflow script: 32e0f9e
• add more CI tests: ce2c68f 4549f25

Bug fixes:

• fixed molecular weight in hypothetical tsv output d83c1b8

And of course all improvements and bug fixes from all v1.3.x patch releases.