Cactus 2.4.4 2023-03-16

Cactus 2.4.4 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.4.4
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.4.4-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.4.4.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.4.4.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.4.4.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 includes some new export tools for the UCSC Genome Browser

• cactus-hal2chains created in order to convert HAL output from Cactus into sets of pairwise alignment chains, using either halLiftover or halSynteny
• cactus-maf2bigmaf created to convert .maf output from cactus-hal2maf to BigMaf and BigMaf Summary files for display on the Genome Browser
• cactus-hal2maf typo fixed where 3 (instead of 30) was set for the default value of --maximumGapLength
• Boost TAFFY normalization defaults in cactus-hal2maf, bringing --maxmimumGapLength to 100, and --maximumBlockLengthToMerge to 1000, and adding the heuristic block-breaking dupe filter from taffy norm. The latter is on by default to prevent over fragmentation, but can be disabled with --kepGapCausingDupes
• Remove --onlyOrthologs and --noDupes options from cactus-hal2maf and replace with the --dupeMode option. --dupeMode single is now the recommended way of getting at most one row / species. More information about this added to the documentation.
• --maxRefNFrac option added to cactus-hal2maf to filter out blocks where the reference sequence is mostly Ns (default to filter out >95% Ns).
• Change abPOA scoring matrix to be more consistent with lastz parameters used by cactus, where N bases are penalized when aligned with other characters. Before, they could be aligned to anything. This will hopefully make the above filter less necessary.
• Fix bug where cactus-blast --restart would not work.