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Cactus 2.0.2 2021-07-07
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@glennhickey glennhickey released this 07 Jul 17:14
· 1714 commits to master since this release
v2.0.2
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Cactus 2.0.2 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 (but don't yet support the Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release notes

This release primarily addresses stability issues during pangenome construction.

Changelog:

  • Use latest abpoa, which fixes bug where aligning >1024 sequences would lead to a segfault
  • Update to Toil 5.4.0
  • More consistently apply filters to minimap2 output in the fallback stage of graphmap-split
  • Build abpoa with AVX2 SIMD extensions instead of SSE4.1 in order to work around instability when building pangenomes. This ups the hardware requirements for releases, unfortunately, as AVX2 is slightly newer.
  • Clean up CAF config parameters
  • Fix CAF secondary filter worst-case runtime issue. It was very rare but could add days to runtime.
  • Slightly tune minimap2 thresholds used for chromosome splitting
  • Normalization option added to cactus-graphmap-join (should be used to work around soon-to-be addressed underalignment bug)
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