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Releases: ComparativeGenomicsToolkit/cactus

3.1.4 2026-02-01

01 Feb 20:06
@glennhickey glennhickey
v3.1.4
00699c2
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3.1.4 2026-02-01 Latest
Latest

Cactus 3.1.4 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).

Release Notes

This release patches some binaries to be a bit faster. It otherwise does not change any logic nor functionality from 3.1.3

  • lastz, minigraph, paffy, taffy and hal now linked with jemalloc
  • paffy updated to version with faster I/O handling
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3.1.3 2026-01-26

26 Jan 19:02
@glennhickey glennhickey
v3.1.3
52bf4f9
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3.1.3 2026-01-26

Cactus 3.1.3 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).

Release Notes

This release resolves a sensitivity issue in Progressive Cactus in the presence of unexpected branch lengths in the guide tree.

  • Take topology into account during greedy outgroup selection. The distance used is now a tuple of (LCA(x,y), dist(x,y)) when computing the distance between x and y (so even if a candiate outgroup is much closer than another in terms of path length, if its lowest-common-ancestor is higher in the tree, it's still considered further).
  • Take uniqueness into account during greedy outgroup selection. Now the path between the ingroup and the first outgroup selected is scaled by 2 when selecting the next outgroup, etc. This is a heuristic to help maximize information in the outgroup set.
  • Revert recent change that only considered leaf nodes for outgroups: ancestors now allowed again.
  • Revert much older change of only using two outgroups: by default three are once again used.
  • Update to vg v1.71.0 and use its simplified interface for anchoring snarls on reference paths
  • cactus_consolidated jobs will now request more memory the more cores they use
  • memory estimates tweaked a bit to better handle large genomes
  • cactus-prepare changed to keep intermediate paf files gzipped, and also to cap the number of tasks in larger alignment rounds.
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3.1.2 2025-12-10

10 Dec 16:12
@glennhickey glennhickey
v3.1.2
42d1c81
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3.1.2 2025-12-10

Cactus 3.1.2 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 addresses one bug from the previous release.

  • Fix cactus-prepare --script regression that caused cactus-blast commands to not be run in parallel.
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3.1.1 2025-12-09

09 Dec 14:22
@glennhickey glennhickey
v3.1.1
291db69
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3.1.1 2025-12-09

Cactus 3.1.1 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 fixes a number of recent bugs, especially from 3.1.0.

  • Fix (still very experimental) --remask option to consider the whole genome when remasking over-masked contigs.
  • Lower maximum nested parallelism to reduce memory footprint of cactus_consolidated
  • Fix automatic branch scaling for ancestors to apply to chaining as well as lastz
  • Add --branchScale option to scale branches
  • Fix --lastTrain bug that could cause crashes in some cases (ex GRCh38 unplaced contigs)
  • Fix crash where reference-guided snarl building couldn't handle stable gaf
  • Update to hal with fixed hal2fasta (when --start specified without --sequence)
  • Fix bug where cactus-prepare could add non-existant --configFile option to cactus-halAppendSubtrees/hal2fasta
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3.1.0 2025-11-27

27 Nov 18:13
@glennhickey glennhickey
v3.1.0
16fae1c
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3.1.0 2025-11-27

Cactus 3.1.0 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 contains several changes to address sensitivity problems with Progressive Cactus.

  • Fix bug where docker run --user $(id -u):$(id -g) did not work with the cactus release docker images
  • cactus-update-prepare regressions fixed (thanks @gwct)
  • Update vcfwave to bring in important patch that fixes a genotype-dropping issue
  • Update to vg 1.70.0. Note that giraffe indexes from this vg won't be compatible with older versions
  • Use reference paths to guide snarl-tree construction (this could lead to better VCFs in very complex graphs)
  • Don't bother writing VCF variants with AC=0, which can arise in some weird cases.
  • Add --lrGiraffe option to produce long-read giraffe indexes
  • Use jemalloc, which significantly improves performance when --consCores is anything higher than about 20
  • Use nested parallelism in BAR stage (together with jemalloc, I've been getting more than a 2X speedup in cactus_consolidated)
  • Add --maskMode option that can toggle between RED and FasTAN for masking in the preprocessor.
  • Update to the latest versions of KegAlign and FastGA
  • More aggressive lastz default parameters. Also reduce branch length thresholds at which more sensitive parameters kick in.
  • Option to re-mask fully-masked contigs with the preprocessor (--remask)

Contributors

gwct
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3.0.1 2025-10-15

15 Oct 11:43
@glennhickey glennhickey
v3.0.1
4e34e49
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3.0.1 2025-10-15

Cactus 3.0.1 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 new functionality

  • Small contigs and N-only contigs no longer sent to FastGA (the latter causes crashes)
  • --mgSplit --lastTrain options fixed to work better together (fixing bug where HPRCv2 graphs would not estimate scores for sex chromosomes)
  • --mgSplit option fixed to output correct .sv.gfa.gz files from cactus-pangenome
  • Toil upgrade to v9.1.2. This fixes a bug that made scripts from cactus-prepare --script fail frequently for no reason on large data sets.
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3.0.0 2025-09-20

20 Sep 17:15
@glennhickey glennhickey
v3.0.0
4838a92
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3.0.0 2025-09-20

Cactus 3.0.0 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 includes several significant patches and updates

  • FastGA support is now more robust and performant
  • MAF normalization and de-duplication bugs fixed
  • cactus-hal2maf interface generalized
  • Toil updated to v9.1.0, which performs much better on Slurm among other improvements
  • Contig naming bug fixed in minigraph (.sv.gfa.gz) output
  • cactus-update-prepare can now rename genomes
  • --delEdgeFilter option added to clip out big edges in pangenoems
  • More realistic ancestral contig sizes, allows kegalign to be run without special config
  • cactus-pangenome --mgSplit option to run minigraph steps independently for each chromosome
  • cactus-prepare --script option added to make a bash script to run pipeline step by step
  • Default outgroup strategy changed to GreedyLeavesPreference (and config XML outgroup toggle fixed)
  • Regression causing cactus-pangenome --vcf (even without --vcfwave) to fail when vcflib not installed fixed.
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2.9.9 2025-06-11

11 Jun 14:22
@glennhickey glennhickey
v2.9.9
3147387
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2.9.9 2025-06-11

Cactus 2.9.9 is available in the following forms:

GPU SUPPORT UPDATE: KegAlign support (--gpu) has been broken since v2.9.3 due to ancestor sizes sometimes outgrowing .2bit's 2Gi contig limit. To work around this issue for this version of Cactus, download the config patch and pass it in with --configFile config-v2.9.9-keg-patch.xml to cactus and/or cactus-align

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 adds FastGA support, along with some bug fixes

  • (prototype) FastGA support added to Progressive Cactus (via --fastga).
  • Fix gpu functionality with singularity binaries
  • Fix cactus-update-prepare to give a valid halRemoveGenomes command
  • Raise an error as soon as empty input FASTA is detected (as opposed to producing empty alignment and eventually crashing)
  • Update to Toil 8.2.0
  • Fix --restart flag bug in cactus-minigraph
  • Fix make error that could (quite rarely) bug out by making a bin file instead of bin/ directory
  • Fix VCF construction crash when multiple VCF references are given, but not all present in every reference contig
  • Update vg to v1.66
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2.9.8 2025-04-15

15 Apr 14:01
@glennhickey glennhickey
v2.9.8
61b873d
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2.9.8 2025-04-15

Cactus 2.9.8 is available in the following forms:

GPU SUPPORT UPDATE: KegAlign support (--gpu) has been broken since v2.9.3 due to ancestor sizes sometimes outgrowing .2bit's 2Gi contig limit. To work around this issue for this version of Cactus, download the config patch and pass it in with --configFile config-v298-keg-patch.xml to cactus and/or cactus-align

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 resolves some issues in Progressive Cactus

  • --queryhspbest=100000 added to default lastz (but not kegalign) parameters in order to prevent tool from taking forever in some worst-case (ie not fully masked) situations
  • paffy chunk fixed to split FASTA contigs across multiple lines (instead of 1 / line). This prevents kegalign crashes on large contigs (which can happen now that ancestors are big).
  • Remove --gpu option from cactus-align. Not only was it inconsistent and unneeded, it prevented cactus-align from even being run from the gpu docker image if no gpus were available.
  • Specify memory to Toil jobs that read in FASTA files (faffy chunk, cacatus_santize_fasta_headers). These tools read entire contigs into memory, and can therefore take non-trivial amounts for large contigs.
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2.9.7 2025-03-17

18 Mar 00:41
@glennhickey glennhickey
v2.9.7
0ae82a5
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2.9.7 2025-03-17

Cactus 2.9.7 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

  • Resolve vcfwave normalization crash on reference chromosomes with zero variation, ex chrEBV.
  • Fix bug introduced in v2.9.6 where per-chromosome outputs could be misnamed.
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