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Cactus 2.6.0 2023-06-09
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@glennhickey glennhickey released this 09 Jun 15:00
· 688 commits to master since this release
v2.6.0
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Cactus 2.6.0 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 updates Cactus's chaining logic which, in early tests at least, allows alignment of T2T-quality assemblies as well as WindowMasked (and not RepeatMasked) genomes.

  • Improved chaining of lastz's PAF output in order to support alignment of T2T-quality genomes
  • Minimum chain length in the Cactus graph now determined by branch length, so that more closely-related genomes can be chained more aggressively while not losing sensitivity along more distant branches where the alignment is more fragmented.
  • Early experiments show that the above changes make Cactus much less sensitive to the input repeat masking. Genomes that previously required masking with RepeatMasker were able to align with the WindowMasking-based fastas directly from NCBI.
  • Update to Toil 5.10.0
  • Update to latest Taffy
  • Specify memory requirements for all Toil jobs (in Progressive Cactus). Cactus Consolidated memory is estimated conservatively, but can be overridden with --consMemory.
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