Skip to content

AMR++ v4 release

Choose a tag to compare

View all tags
@meglab-metagenomics meglab-metagenomics released this 15 Sep 21:23
· 70 commits to master since this release
v.4.0.0
fded607
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Verified
Learn about vigilant mode.

Official release of AMR++ v4.

What's Changed in this Release

  • New SNV Calling Module (--pipeline bam_snv): Integrated a complete metaSNV and NGLess variant-calling workflow (modules/SNV/metasnv.nf), allowing for single-nucleotide variant identification and matrix generation from aligned BAM files.
  • Resistome-Based SNV Filtering: Added optional post-processing (Filter_SNV_matrix.py) to cross-reference SNV calls against confirmed gene presence in the resistome matrix (snv_filter_by_resistome = "Y").
  • Updated Container Images: Updated the Docker image (and associated Singularity/Apptainer profiles) to include all dependencies required for metaSNV, NGLess, and updated Python parsing scripts.
  • MEGARes v4.00 Support & Documentation: Updated default annotations to MEGARes v4.00 and added a new step-by-step tutorial for SNV calling (docs/SNV_calling_tutorial.md).

For a detailed breakdown of all changes, please refer to the CHANGELOG.

Assets 2
Loading