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Cactus 2.7.0 2023-12-05
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@glennhickey glennhickey released this 05 Dec 23:51
· 219 commits to master since this release
v2.7.0
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Learn about vigilant mode.

Cactus 2.7.0 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 changes how outgroups are used during chaining during progressive alignment, and adds some pangenome options

  • Add --xg option for xg pangenome output.
  • Add (experimental) cactus-pagnenome --noSplit option in order to bypass reference chromosome splitting. This was previously only possible by running step-by-step and not using cactus-graphmap-join.
  • Add pangenome tutorial (developed for recent hackathon) to documentation.
  • Update to vg version 1.53.0.
  • Updated local alignment selection criteria. At each internal node of the guide tree Cactus picks a set of pairwise local alignments between the genomes being aligned to construct an initial sequence graph representing the whole genome alignment. This sequence graph is then refined and an ancestral sequence inferred to complete the alignment process for the internal node. The pairwise local alignments are generated with LASTZ (or SegAlign if using the GPU mode). To create a reliable subset of local alignments Cactus employs a chaining process that organizes the pairwise local alignments into pairwise chains of syntenic alignments, using a process akin to the chains and nets procedure used by the UCSC Browser. Previously, each genome being aligned, including both ingroup and outgroup genomes, was used to select a set of primary chains. That is, for each genome sequence non-overlapping chains of pairwise alignments were chosen, each of which could be to any of the other genomes in the set. Only these primary chains were then fed into the Cactus process to construct the sequence graph. This heuristic works reasonably well, in effect it allows each subsequence to choose a sequence in another genome with which it shares a most recent common ancestor. In the new, updated version we tweak this process slightly to avoid rare edge cases. Now each sequence in each ingroup genome picks primary chains only to other ingroup genomes. Thus the set of primary chains for ingroup genomes does not include any outgroup alignments. The outgroup genomes then get to pick primary chains to the ingroups, effectively voting on which parts of the ingroups they are syntenic too. The result of this change is that the outgroups are effectively only used to determine ancestral orderings and do not ever prevent the syntenic portions of two ingroups from aligning together.
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