New tool: vConTACT2 a tool to provide taxonomic context of metagenomic sequencing data #7646
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
The default selection of tool for each step seems strongly recommended.
Add support for legacy vContact-PC files. Fill out help section. Add tests.
SaimMomin12
reviewed
Feb 3, 2026
Contributor
SaimMomin12
left a comment
SaimMomin12
left a comment
There was a problem hiding this comment.
Some comments inline.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
FOR CONTRIBUTOR:
I started wrapping this tool before I noticed that vConTACT3 was in development, but I think this version would still be useful to have for now. The main change with version 3 seems to be the portable handling of reference databases. I think that would require a data manager, something I have no experience with.
Also, would it be better to drop the '2' from the tool id to make later upgrades more seamless? I only kept it because vConTACT2 and vConTACT3 have different package names too.