bakta

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ValueError: Need a Nucleotide or Protein alphabet

8

Hi, I try to use bakta desktop, which is working fine to some extent (I get gff and all the prediction part works fine), however i got the following error...

kitka2000

Macromolecular structure and integron annotation, custom features

2

**Is your feature request related to an existing issue or bug?** no **Is your new feature related to a general problem?** Typically annotation of large secretion systems (T3SS, T4SS, T6SS,...

alexweisberg

Add IS element detection

2

Bakta needs an `IS` element detection and annotation feature. A promising candidate (detection, annotation, recently updated, BioConda) is `ISEScan`: - https://github.com/xiezhq/ISEScan - https://doi.org/10.1093/bioinformatics/btx433

oschwengers

Improve annotation of phage-borne genes

1

Pre-annotation of UniRef90 clusters could be improved using a dedicated phage database like: - VOGDB: http://vogdb.org/download - PHROGs: https://phrogs.lmge.uca.fr/READMORE.php

oschwengers

Question regarding annotation

1

Hello! I have annotated a few of my complete genomes with Bakta version 1.3.3 and bakta db version 3.1, using the following command: ``` bakta --threads 4 --prefix $outfile --complete...

hkaspersen

Annotate all clusters by KEGG's KoFams: https://www.genome.jp/ftp/db/kofam/

oschwengers

a lighter database?

1

Hi there and thank you for the tool, is there an option to download only part of the database? https://zenodo.org/record/5961398/files/db.tar.gz) is nearly 30GB and it takes about 12 hours to...

GaioTransposon

gene ontology cross-annotation mapping

6

Congrats on the release. I already tried bakta on a couple genomes I was studying and the results are really good, without being much slower than prokka. (output also works...

rsiani

Add prediction of transcription terminators

1

Add detection/prediction of Rho (in)dependent translation terminators ## Rho independent - transtermhp: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-2-r22; Bioconda:https://anaconda.org/bioconda/transtermhp

oschwengers

Superseede UniRef100/UniRef90 annotations by the following specialized plasmid protein DBs: Mobilization proteins: - **MobScan**: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937521 https://castillo.dicom.unican.es/mobscan_about/ https://castillo.dicom.unican.es/mobscan_about/MOBfamDB.gz Conjugation proteins: - **CONJScan** https://github.com/gem-pasteur/Macsyfinder_models/tree/master/models/Conjugation http://dx.doi.org/10.1371/journal.pone.0110726 http://dx.doi.org/10.1038/srep23080

oschwengers