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Cactus 2.8.0 2024-03-13
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@glennhickey glennhickey released this 13 Mar 17:16
· 304 commits to master since this release
v2.8.0
7286b49
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Cactus 2.8.0 is available in the following forms:

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 significantly changes the preprocessor step of Progressive Cactus in order to be more robust and efficient in the presence of unmasked repeats, something that seems more prevalent with newer, T2T assemblies.

  • Replace lastz repeatmasking with REepeat Detector (RED) in the Progressive Cactus preprocessor. RED is more sensitive and orders of magnitude faster than the old lastz masking pipeline. Crucially, it is able to mask regions that would slip by RepeatMasker/WindowMasker/lastz in new T2T ape genomes that would otherwise break Cactus downstream. Tests so far show this change to make Cactus much faster and more robust. The old lastz pipeline can still be toggled back on in the config.
  • Delete many unneeded files that previously collected in the jobstore directory until the end of execution. This was a particular issue in large cactus-pangenome runs where the jobstore would creep up to several terabytes for HPRC-sized inputs.
  • No longer require manually editing the blast chunksize in the config when running on Slurm (to reduce the number of jobs). It's now scaled up automatically on slurm environments (by a factor controlled in the config).
  • Fix bug introduced in last release where Cactus would not work on AWS/MESOS clusters unless --defaultMemory and --maxMemory options were specified (and in bytes).
  • Update to the latest taffy and vg
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