Oliver Schwengers

Idea for potential runtime improvements

7

Hi Benjamin, thanks a lot for developing and maintaining diamond. By monitoring tons of Diamond runs from Bakta (2k=80% query/subject coverage, --fast), I saw that a significant proportion of the...

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

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

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

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

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

Let's try if [Pyrodigal](https://github.com/althonos/pyrodigal) might be a suitable, faster and most important actively maintained successor to Prodigal.

Absolute target for *latest* symbolic link

2

Hi and thanks for developing and maintaining AMRFinder! We use AMRFinder within Bakta and we quite often get filed issues when people move their Bakta database containing an instance of...

Lost IS name & family information

1

First: thanks so much for making this DB available! With the last commit something happened to the protein file `IS.faa`. Example: DNA: `>IS-LL6_IS3_IS3` AA: `>html.2020//IS-LL6 ~~~html.2020//IS-LL6_unknown_unknown_ORF~~~Transposase~~~` 1. IS names are...

Add median to hist summary

1

Hi and thanks for this very useful tiny tool! In addition to min/mean/max, could you also add the median to the hist summary?