Hi everyone,
We developed VAT to solve a specific frustration: the fragmentation of alignment tools. Usually, you need one tool for short reads, another for long reads, and different workflows for homology search or WGA. VAT generalizes seeding and indexing strategies into a single architecture that handles all of these.
We have tested it on standard datasets, but I know the Biostars community has the wildest, messiest, most edge-case-filled data out there. I am looking for beta testers to try running VAT on their pipelines and report any crashes, weird alignment artifacts, or segfaults.
Availability: The tool is ONLY free for academic and research use. VAT Link
If you run into any issues, please open an Issue on GitHub. I am actively monitoring the repo and aiming to fix bugs.
Thanks for your time and help!
Hao
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It looks like you deleted a prior version of this post to put it up again in more or less its original form. Normally biostars does not allow posts to be deleted once they receive a comment/answer (prior post had 3 comments). Please do not delete posts in future that have received at least one comment/answer.
Look @OP, if users already comment on your post then out of basic respect, don't delete it.
@Dave Carlson asked
I asked
Thanks for your reply. I am sorry for deleting the prior version of post. We have no plan to open source code.
Then good luck getting help from a community dedicated to open source and peer review. I also see no response to the actual questions I asked, so I see this as an attempt to get free help rather than providing anything actually useful for the community.
I am sorry for this.
Current version (as of end of Jan 2026) of the manual (https://github.com/xuan13hao/VAT/blob/main/data_preparation/VATmanual.pdf ) shows two ouput options. One is some kind of a table (blast like I suppose) and a binary alignment archive (
.vatr) which would make this a non-starter as input for standard analysis tools/genome viewers. At a minimum start supporting SAM/BAM/CRAM format output for NGS data and/or provide a converter for.vatrfiles.Note: Since the tool requires AVX2, it is not for Apple M* CPU users.
Thanks for your feedback. I will support BAM format.