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StaPH-B
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
### What container were you trying to use, and how were you attempting to use it? Is anybody know why the tool doesn't work when I give in input the...
### What tool are you looking for and why? Mentioned by @SESchmedes on SLACK. Dorado basecalls nanopore data. There does not seem to be a biocontainers image, although there is...
### What tool are you looking for and why? Medaka is on biocontainers, which is fine, but biocontainers lags behind the current version by a bit. Medaka's license is as...
### What container needs an update? There's a newer version of skesa! Well, not really. It looks like skesa itself is still being called version 2.4.0, but saute is now...
### What tool are you looking for and why? The biocontainers image works great, but we don't currently have this one on StaPH-B
This PR will close #661 This PR adds a dockerfile for Kaptive v2.0.7 and adds a new database for Vibrio parahaemolyticus locus typing. Differences from previous dockerfile: - Added Vp...
### What container needs an update? There's a new version of HMMER! http://cryptogenomicon.org/hmmer-3-4-release.html > Supports native ARM / Apple Silicon acceleration.
### What tool are you looking for and why? [USHER](https://github.com/yatisht/usher) is a tool that can be used on its own for phylogenetic tree creation.
### What container needs an update? Orthofinder has a new version! https://github.com/davidemms/OrthoFinder/releases/tag/2.5.5 A lot has improved since the version in this repo. The [Dockerfile](https://github.com/StaPH-B/docker-builds/blob/master/orthofinder/2.17/Dockerfile) from 2.17 is going to need...
### What container needs an update? Metaphlan has a new version out! https://github.com/biobakery/MetaPhlAn/releases/tag/4.0.6 It looks like it's mostly to keep up with changed in taxonomic assignments (especially significant for Klesbiella...