v1.3.1

This is the first v1.3 patch release (v1.3.1).

Bug fixes:

• fixed the locus-tag checks: use a more relaxed format as default and INSDC restrictions on --compliant: e2651c3 (Thanks @taylorreiter)
• skip /pseudo annotated genes in --proteins-provided GenBank files: 0f0165d (Thanks Charlotte Reuschel)

v1.3 - Quo vadis, protein?

This is the third minor release (v1.3) introducing a new feature and many improvements and bug fixes.

Compatible database scheme version: 3

New features:

• prediction of signal peptides via DeepSig: #32 (Thanks @Anna-Rehm)

Improvements:

• provide summary with genome & annotation statistics as .txt file: #88 (Thanks @hkaspersen)
• accept user provided proteins in GenBank format: #89 (Thanks @Tonny-zhou)
• removed alignment gaps (-) in input sequences: #87 (Thanks @RotimiDada)
• improved sORF overlap filter runtime performance: cb204fb
• improved outputs: 76e07a4 90bfe99
• added more checks & tests: b779e1f 4e6c35d f4103f0 08ebb03 1672a87 26a8ed2
• added --gram to CWL file: 2246319

Bug fixes:

• fixed tmRNA predictions that cross sequence origins: #90 (Thanks @LuisFF)
• moved oriC/T/V product to Note in INSDC and compliant GFF3 outputs: 2f5cb1d 716302e 5e1a0d8
• fixed sequence description on Fasta import: bfdf67f
• fixed Fasta import log error: 5209672
• fixed EDAM out types in CWL file: a1a0ad1

And of course all improvements and bug fixes from all v1.2.x patch releases.

v1.2.4

This is the 4th v1.2 patch release (v1.2.4) fixing a database download issue.

Bug fixes:

• fixed the database download/update logic by restoring an accidentally removed URL: 247a047 (Thanks @andreaniml)

v1.2.3

This is the third v1.2 patch release (v1.2.3) providing some minor improvements and a bug fix.

Compatible database scheme version: v3

Improvements:

• added several CI argument tests: e26b5f5 f5c57ef af20f66 dfc9a66 a37b5b5
• added locus and locus-tag prefix argument checks: 842437b 31fd72e c530e4c 8e27f68 8c58851
• polished readme and error messages
• added citation information

Bug fixes:

• fixed the creation of a user defined tmp directory: 753e6e8

v1.2.2

This is the second v1.2 patch release (v1.2.2) providing a couple of improvements and bug fixes.

Compatible database scheme version: v3

Improvements:

• set BLAST_USAGE_REPORT environment variable to false forestalling blastn to hang for 90 secs if no internet connection is available
• add a check for duplicated input sequence IDs: 888bb9b (Thanks @joyn-sromero)
• add further SQLite URI parameters to improve read-only access: e658a2e
• synchronize Conda environment dependencies and runtime dependency version checks: 95ef71f c516656
• add AMRFinder protein hits to dbxref outputs: 505a2ce

Bug fixes:

• fix NA issue on HMM-only AMRFinder hits: 71e2dac e9ff01c (Thanks @taylorreiter)

v1.2.1

This is the first patch release (v1.2.1) merely fixing a wrong former version tag (v1.1.2).

v1.2.0 - User provided proteins arrived ...

This is the second minor release (v1.2.0) introducing user provided proteins as well as many improvements.

Compatible database scheme version: 3 v3.0

New features:

• introduce --proteins accepting a user provided set of trusted protein sequences: 992d929 1541f10 691646d (Thanks to @Tonny-zhou)

Improvements:

• revise Dbxrefs for UniParc & UniRef: 02b5dc8
• revise truncated dnaA/repA genes on rotated replicon sequences: 0c4ad10 (Thanks to Jochen Blom)
• assign locus tags to gene features only: c1e1c05
• extract nt seqs for ncrna-regions: f77e308
• generate unique feature IDs used as ID in GFF3: df32038
• add products to oriC/oriV/oriT features: 2eabd93
• reduce numbers of similar to aa sequence inference qualifiers in INSDC outputs to 1: 16401da
• improve and fix CWL file: 6776ca7 1d18e77 5c80d15
• exrtact & store Pfam HMM hits on hypothetical proteins: 2ba985a

v1.1.1

This is the first v1.1 patch release (v1.1.1) providing a couple of improvements and minor bug fixes.

Compatible database scheme version: v3

Improvements:

• added a revision & refinement logic for gene symbols: 539137b
• added further CDS product revision rules: f8ec2aa 1fcca89 8915af7 626981b 321391b 0d93c2f #69 (Thanks @michoug)

Bug fixes:

• fixed AMRFinderDB issue in docker shell script: e825361
• fixed None values of CDS rbs_motif attributes: 0727b25
• skip CDS annotation if no CDS are predicted: 3787e01
• fix several CDS product revision rules

v1.1 - INSDC submission & annotation of MAGs: Hey! Ho! Let's go

This is the first minor release (v1.1) introducing several new features, many improvements and countless bug fixes.

Compatible database scheme version: 3 v3.0

New features:

• add new --compliant option for INSDC genome submissions: #69 (Thanks @michoug)
• introduce PSCCs (UniRef50) as a fallback if PSCs (UniRef90) are not detected, greatly improving the annotation of less represented species and metagenome-assembled genomes (MAGs): 84c808f
• export nucleotide sequences: #57 (Thanks @mcroxen)
• revise suspect CDS product names: f85970b

Improvements:

• various improvements and fixes in GFF3, GenBank and EMBL files to adhere to INSDC specs: #69
• improve internal DB download: bdd665a
• use Diamond version v2.0.11 and its --fast option: c82f4e2 19c95d8 (Thanks to @bbuchfink for bbuchfink/diamond#419)
• use stable CLI progress library alive-progress 0ac5625
• improve GFF3 output regarding GFF3 specs: 697121f
• store AMRFinderPlus DB within the Bakta DB directory: 04ff7b0 (Thanks to @LuisFF)
• redirect BAKTA-TMP directory to AMRFinderPlus to prevent stale files: 26f81fc
• detect & mark tmRNA on sequence edges: 782f640
• adhere to translation table in tmRNA prediction: 450d6b7

Bug fixes:

• fix var name in Docker shell script: e6bab09 (Thanks @joyn-sromero)
• fix inflated blastn thread numbers: e9073e1 (Thanks @LuisFF)
• fix location of features on sequence edges: 34873e7
• fix BLAST+ tool name in GFF3: efff065
  and many more ...

v1.0.4

This is the fourth v1.0 patch release (v1.0.4) fixing a couple of minor bugs and adding further minor improvements.

Compatible database scheme version: v2.0

Bug fixes:

• fixed an hmmsearch error if no CDS/sORF remain as hypotheticals: 9d4fc71 (Thanks Matthew Croxen)
• fixed a threadpool issue upon single core executions: 631fac6

Improvements:

• added GFF3 feature IDs to features w/o locus_tag: 08b8eae (Thanks @ZarulHanifah #54)
• add clipping of UniParc DB prefixes: c861af8 (Thanks Jochen Blom)