Cactus 2.9.1 2024-09-25

Cactus 2.9.1 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.1
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.1-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.9.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.9.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.9.1.tar.gz
  Install instructions in README.md

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

The Docker images and binaries linked above are built using AVX2 extensions, and require a CPU that supports them, except the "Pre-compiled Binaries For Older CPU Architectures" which should be compatible with any 64-bit architecture (and, since version 2.3.1, support Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release Notes

This release updates the pangenome pipeline, and adds KegAlign to progressive cactus.

• GPU lastz implementation changed from SegAlign to KegAlign, and should be more robust and better supported as a result.
• Path normalization added to pangenome pipeline to make sure no two equivalent alleles through any site have different paths. AT fields in VCF should now always be consistent with the graph as a result.
• Always chop nodes to 1024bp by default in pangenome pipeline. This ensures that all outputs (gfa, gbz, vcf etc) have compatible node ids. Before, only GBZ and downstream graphs were chopped which was too confusing. Old logic can be re-activated using the config XML though.
• Fix recent bug where using the --mgMemory option would crash cactus-pangenome
• (Experimental) --collapse option added to pangenome pipeline to incorporate nearby self-alignments, including on the reference path.
• Left shifting VCFs (bcftools norm -f) no longer run by default (except on vcfwave-normalized outputs), since it can cause conflicts with PanGenie by writing multiple variants at the same location.