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 ...