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Cactus 2.5.2 2023-05-15
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@glennhickey glennhickey released this 15 May 20:13
· 760 commits to master since this release
v2.5.2
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Cactus 2.5.2 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 patches some bugs in the pangenome pipeline and makes it a bit more user-friendly

  • Fix support for multiple referenes via --reference and --vcfReference
  • Fix bug where certain combinations of options (ie returning filtered but not clipped index) could lead to crash
  • Fix crash when handling non-ascii characters in vg crash reports
  • Fix the --chrom-vg option in cactus-pangenome
  • New option --mgCores to specify number of cores for minigraph construction (rather than lumping in with --mapCores which is also used for mapping)
  • Better defaults for number of cores used in pangenome pipeline on singlemachine.
  • Fix bug where small contigs in the reference sample could lead to crashes if they couldn't map to themselves (and --refContigs was not used to specify chromosomes). --refContigs is now automatically set if not specifed.
  • Update to vg 1.48.0
  • Update pangenome paper citation from preprint to published version.
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