v1.9 - Here's my region of interest

This is the ninth minor release (v1.9) introducing user-provided feature regions and various minor improvements.

Compatible database scheme version: 5

New features

• Support a priori user-provided feature regions via --regions either in Genbank or GFF3 format (currently, only CDS features are supported). CDS coordinates are imported, supersede de novo predicted CDS, and are subject to the regular internal annotation workflow. To provide functional annotation, as well use --proteins: #216 #245 #247 #250 #259 (Thanks @marade @PengfanZhang @simone-pignotti @thorellk)

Improvements

• Extract & export CRISPR spacer & repeat sequences: #171 #249 (Thanks @alexweisberg)
• Add support for Pyrodigal v3: #240 #244 (Thanks @jsgounot)
• Replace HMMER with PyHMMER: #219 (Thanks @jhahnfeld)
• Re-activate parallel pyrodigal gene prediction: #252 (Thanks @althonos)
• Introduce auxiliary scripts: #246 #251 (Thanks @AhmedElsherbini)
• Add Podman wrapper script: bd50faa
• Update dependencies to latest versions: 3260441 33c02f9 a1d2ffe b265672 1a2c48e

Fixes

• Fix PyPI CD: #231
• Add missing --force parameter to Docker wrapper script: f39434e
• Fix wrong runtime report: #243

Full Changelog: v1.8.2...v1.9.0

v1.8.2

This is the second v1.8 patch release (v1.8.2).

Improvements:

• Replacd HMMER by PyHMMER: 3415e89 (Thanks @jhahnfeld)
• Refactored & improved CI scripts
• Refactored the code
• Tweaked code to expand required BioPython versions: 6a88c4b (Thanks @alexweisberg)
• Deactivated --force parameter for the current working directory`: a039bec
• Added Pyrodigal to dependency checks: 17bcfc9

Bug Fixes:

• Fixed and improved the CWL wrapper: #221 #229 #230 (Thanks @bartns & @jjkoehorst)

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