Cactus 2.9.4 2025-02-27

Cactus 2.9.4 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.4
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.4-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.9.4.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.9.4.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.9.4.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 fixes compatibility with newer Python versions and improves the --vcfwave option, along with a few other patches

• vcfwave more parallelized (on chunks rather than whole-chromosome)
• vcf normalization turned on by default after vcfwave, including allele merging from collapse_bubble package
• fix --defautCores option
• fix compatibility with Python 3.13
• update to vg 1.6.3
• update Toil to 8.0.0
• add --snarl-stats option to print a table of large bubbles and their reference coordinates
• default ancestral genome construction parameters changed to give larger, more contiguous ancestors
• update to gfaffix 0.2.0
• fix recent regression where non-agctn IUPAC fasta characters would cause errors in cactus_sanitizeFastaHeaders, they are now read in as Ns (once again)
• minigraph graph (.sv.gfa.gz) now output with PanSN names, as opposed to Cactus's internal id=event| prefix.
• use more sensitive seeds for abPOA's progressive ordering
• reference genomes now added by mash distance order (instead of always first) by default. this behaviour can be adjusted in the config with minigraphSortInput and minigraphSortReference.