Bakta

New features:
- add new `--compliant` option for INSDC genome submissions: https://github.com/oschwengers/bakta/issues/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): https://github.com/oschwengers/bakta/commit/84c808fb343cadb36b4afdbdd56dbf416b7512e3
- export nucleotide sequences: https://github.com/oschwengers/bakta/issues/57 (Thanks mcroxen)
- revise suspect CDS product names: https://github.com/oschwengers/bakta/commit/f85970b7a9b6a55336b91570955777c062f03852

Improvements:
- various improvements and fixes in GFF3, GenBank and EMBL files to adhere to INSDC specs: https://github.com/oschwengers/bakta/issues/69
- improve internal DB download: https://github.com/oschwengers/bakta/commit/bdd665aa87bcb14d7ddaba22744b45f9b700b74a
- use Diamond version v2.0.11 and its `--fast` option: https://github.com/oschwengers/bakta/commit/c82f4e21aae75ecc8d48146aab8499c5967d8b1b https://github.com/oschwengers/bakta/commit/19c95d802cd038500e53fdfa30353420c89f5480 (Thanks to bbuchfink for https://github.com/bbuchfink/diamond/issues/419)
- use stable CLI progress library [alive-progress](https://github.com/rsalmei/alive-progress) https://github.com/oschwengers/bakta/commit/0ac56256dda51e16fabce08b4500048bd1ea5d79
- improve GFF3 output regarding GFF3 specs: https://github.com/oschwengers/bakta/commit/697121f6192bbee883b3102578891d2de6beb2db
- store AMRFinderPlus DB within the Bakta DB directory: https://github.com/oschwengers/bakta/commit/04ff7b00c0b4b71738072710355a45a8f9fa8137 (Thanks to LuisFF)
- redirect BAKTA-TMP directory to AMRFinderPlus to prevent stale files: https://github.com/oschwengers/bakta/commit/26f81fcc82e1001ce2021011fcbb40416a9c11c2
- detect & mark tmRNA on sequence edges: https://github.com/oschwengers/bakta/commit/782f640f920368216920f9bf8d0ff4f219c3d91d
- adhere to translation table in tmRNA prediction: https://github.com/oschwengers/bakta/commit/450d6b7224469e4bf39cbad9ac24d3e9e3dbc9f1

Bug fixes:
- fix var name in Docker shell script: https://github.com/oschwengers/bakta/commit/e6bab09dba5ff9ea478242edb6b2863e5dd2e122 (Thanks joyn-sromero)
- fix inflated blastn thread numbers: https://github.com/oschwengers/bakta/commit/e9073e188c5888701bbcf5ab800058d191384463 (Thanks LuisFF)
- fix location of features on sequence edges: https://github.com/oschwengers/bakta/commit/34873e7bb91984a34d43d69bf2eb9b24573ab289
- fix BLAST+ tool name in GFF3: https://github.com/oschwengers/bakta/commit/efff065f212f9a627995291b0590f8bc6e55b9fb
and many more ...

Bug fixes:
- fix calculation of GC & N50 stats: https://github.com/oschwengers/bakta/commit/2829a24c7a01c94bcd4bf7d93319f2139b10765f (Thanks Matthew Croxen)
- fix a typo in GenBank/EMBL output: https://github.com/oschwengers/bakta/commit/1595133c2aede5a853397b0499c123676905d6e7 (Thanks davised)

Improvements:
- download/update AMRFinderPlus db upon Bakta db download/update: https://github.com/oschwengers/bakta/commit/94ccc695e2604dce19581d5bd1d2ed46f02d28c9
- add a short note to error msg if AMRFinderPlus db is not available: https://github.com/oschwengers/bakta/commit/750396feff7edb12c4e4c96e3c1ee2a15470adac
- add more sORF unit tests: https://github.com/oschwengers/bakta/commit/685a3bc045f4fec51d96f6d754989b5c9c31601b
- fix link to old db files: https://github.com/oschwengers/bakta/commit/140e34884ce555590cccef70bb8757562bcb463b (Thanks davised)
- readme updates & improvements

This is the first v1.10 patch release (v1.10.1).

Improvements
- Improved handling of draft genome in circular plots: 01189833cf70ca9f1fe9e72773f7521a7bf729f0
- Added N90 to genome statistics: 7abfa9aa59e791104f652db316267f1635f408c5

Fixes
- Fixed changed Micromamba parameter in Dockerfile: 342 345 (Thanks pamelacamejom / mjfos2r)
- Fixed INSDC `note` qualifiers: 346 (Thanks Dx-wmc)

This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements.

Compatible database scheme version: 5

Important
Since v1.10.0, Bakta requires Python `>=3.9`, uses [pyCirclize](https://github.com/moshi4/pyCirclize) instead of Circos, and discarded support of [DeepSig](https://github.com/BolognaBiocomp/deepsig)!

An important decision had to be made for this release regarding supported Python versions, external dependencies and features impacted by this. Both Circos and [DeepSig](https://github.com/BolognaBiocomp/deepsig) seem to be _out of support_ for a long time. Hence, Circos was replaced by [pyCirclize](https://github.com/moshi4/pyCirclize), a pure-Python actively-maintained library, enabling a couple of new features. As a result, Bakta's Python dependency had to be bumped to `>=3.9`, thus unfortunately loosing compatibility with [DeepSig](https://github.com/BolognaBiocomp/deepsig). Dropping an existing feature feels odd and wrong, but as a developer, sticking to unmaintained external software for too long constantly increases your daily pain level and slows down the project as a whole. This hasn't been an easy decision, but a necessary. So, If you depend on the detection of signaling peptides, please keep using Bakta `<=v1.9.4`.

New features
* Accept user-provided trusted HMMs via `--hmms`: 309 327 (Thanks StefDiV)
* Recover output files based on Bakta's comprehensive `JSON` output via `bakta_io`: 304 339 (Thanks cpauvert)
* Write annotation inference metrics to new `*.inference.tsv` file: 314 331 (Thanks jvera888 / gbouras13)
* Deactivate feature overlap filters via `--skip-filter` : 295 (Thanks Daniel-Tichy)

Improvements
* Support translation table `25`: 323 (Thanks ndombrowski)
* Export CRISPR and tRNA nucleotide sequences: 336 (Thanks YoungerRen)
* Replacement of Circos by [pyCirclize](https://github.com/moshi4/pyCirclize): #344 (Thanks acarafat / alexweisberg)
* Introduce `--label`, `--size` and `--dpi` parameters in `bakta_plot` to customize plots: 344
* Add fixes for common submission errors: 330 (Thanks kevinmyers)
* Improve INSDC compliance: 30b3928d62cab771f1b8f524946ba7c4aef9acf2 8ba8a146232861c28243b86f91624f4f455e042c
* Reduce the locus tag offset from 5 to 1 and allow specifications via `--locus-tag-increment`: 279 (Thanks 1996xjm)
* Revise internal/external designation of truncated features and (real) pseudogenes: 333
* Print msg if IPS and pseudogene detection is skipped using the db `light` version: 320 (Thanks flashton2003)
* Review internal main data structure: 338

Fixes
* Fix import of user-provided CDS spanning sequence edges: 324 332 (Thanks aekazakov)
* Fix translated protein sequences for CDS truncated at both sides: 340 (Thanks tpillone)
* Fix wrong truncation label: 341
* Fix import of user-provided regions in combination with a metadata replicon table: 326

**Full Changelog**: https://github.com/oschwengers/bakta/compare/v1.9.4...v1.10.0

This is the fourth v1.9 patch release (v1.9.4).

Fixes
- Fixed CDS gene translation in meta mode: 301 (Thanks ohickl)
- Fixed the CRISPR parser for short (<10 nt) spacer sequences: 299 302 (Thanks ohickl)
- Fixed Pyrodigal and Pyhmmer version detection: 294 (Thanks EricDeveaud)

Improvements
- Skip certain genes in user-provided regions: 288 303 (Thanks Dx-wmc)

This is the third v1.9 patch release (v1.9.3).

Fixes
- fixed a regex in the CRISPR parser skipping spacers in some special cases: c7478033265ccb2218582f9d3121825dbf7ce91a 265 (Thanks ZarulHanifah)
- fixed wrong Piler-CR CRISPR array stop position omitting the last spacer: 276
- tmp. pinned Diamond version to `v2.1.8` due to an upstream bug: 0dd84fb60d9fc03c280287af1d237da2fd7d74db

Improvements
- added parent ID to CRISPR repeat/spacer features in GFF3 outputs: ae71c09199981004db8c870d198e8ce11b2e60f8