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Cactus 2.5.0 2023-04-03
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@glennhickey glennhickey released this 03 Apr 22:39
· 825 commits to master since this release
v2.5.0
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Cactus 2.5.0 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 greatly simplifies the interface for building pangenomes

  • Introduction of cactus-pangenome command that, like cactus for the progressive aligner, runs the whole pipeline in one shot. Its inputs are a list of fasta sequences and sample names and it outputs the pangenome graph and various indexes, vcf, etc. Intermediate outputs are exported at the end of each stage, so low-level commands can be used to repeat or continue the workflow.
  • # characters in fasta contig names no longer need to be cleaned out with special invocation of cactus-preprocess to avoid conflicts with vg indexes. This now happens automatically within the pipeline.
  • The lower level pangenome commands are all still supported and documented. But cactus-align-batch is now deprecated. This means it is removed from the documentation (except when describing older results) and from continuous integration tests, and it will give a warning when used. Users should now just run cactus-align instead of cactus-align-batch where applicable, using the former's --batch option. cactus-align-batch was a hack required to scale up before the cactus v2.0 rewrite but used nested Toil workflows and needed to go.
  • Documentation updated to focus on the simpler interface
  • GFAffix updated to fix a rare crash
  • cactus-graphmap-join (and cactus-pangenome) will not fail in the event a VCF indexing error (ex from chromosomes that are too long for tbi). Instead it will give a warning and produce no index.
  • New cactus-hal2maf option --keepGapCausingDupes is changed to --filterGapCausingDupes and turned off by default. The underlying code has bugs that cause problems on certain datasets, and is not ready to be activated by default.
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