Oliver Schwengers

@[email protected]
53 Followers
56 Following
31 Posts
Microbial bioinformatics, WGS bacteria, plasmids, PostDoc @JLUGiessen, father of 2, husband, astrophotographer
Twitterhttps://twitter.com/oschwengers1
GitHubhttps://github.com/oschwengers
ORCiD0000-0003-4216-2721
Oliver SchwengersNov 29, 2023
And for the sake of completeness, there's already a v1.9.1 patch release catching 2 minor bugs 😆
https://github.com/oschwengers/bakta/releases/tag/v1.9.1
(7/7)
Release v1.9.1 · oschwengers/bakta

This is the first v1.9 patch release (v1.9.1). Fixes Fixed a Python KeyError when both --regions and --keep-contig-headers are used: d3d7a98 (Thanks @thorellk) Fixed a bzip2 error in the Docker bu...

GitHub
Oliver SchwengersNov 29, 2023
We replaced HMMER with PyHMMER, and updated to Pyrodigal to v3.1. Furthermore, we bumped various dependencies to most recent versions.
(6/7)
Oliver SchwengersNov 29, 2023
We introduce auxiliary scripts for common downstream tasks as for example the extraction of annotations for certain sub regions or the aggregation of annotation stats of multiple genomes. Ideas, contributions & PRs are highly welcome!
(5/7)
Oliver SchwengersNov 29, 2023
Bakta now annotates and exports spacer and repeat sequences within CRISPR arrays.
(4/7)
Oliver SchwengersNov 29, 2023

Currently, only import of CDS coordinates are supported, but more might come later.

BTW, to additionally provide functional annotations of these CDS, you can provide related aa sequences with custom annotations via --proteins.
(3/7)

Oliver SchwengersNov 29, 2023
We introduce a new --region parameter supporting user-provided pre-annotated feature regions in Genbank/GFF3 format.
For example, CDS coordinates are imported, supersede ab initio-predicted CDS, and then are subject to the regular internal annotation workflow.
(2/7)
Oliver SchwengersNov 29, 2023

🦠🧬💻 Just released Bakta 1.9.0 with new features & various improvements:

- new --regions option to provide pre-annotated feature regions
- annotation of spacer & repeat sequences in CRISPR arrays

https://github.com/oschwengers/bakta/releases/tag/v1.9.0

More information below 👇 (1/7)

Release v1.9 - Here's my region of interest · oschwengers/bakta

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 f...

GitHub
Oliver SchwengersMay 31, 2023
We fixed some rare occasions of wrong 5' / 3' ("prime") characters in product descriptions causing issues in downstream analyses. (6/6)
Oliver SchwengersMay 31, 2023
Now "bakta_proteins" writes its full annotation results as a comprehensive JSON - just like the main workflow. (5/6)
Oliver SchwengersMay 31, 2023
Compatibility with NCBI Bankit was improved:
- setting genome sequences' attributes "location" and "plasmid-name" (explicitly or auto-generated)
- removing strain designation from "organism"
(4/6)