Issues

• Explicitly specify the haplotype in seqfile rather than parsing from the assembly name

  ComparativeGenomicsToolkit/cactus#2048 · Filter by author diekhans opened on Oct 19, 2026

• High hal2vg memory usage with 1,319 human haplotypes

  ComparativeGenomicsToolkit/cactus#2047 · Filter by author yeeus opened on Oct 19, 2026
  4

• halRemoveGenome causes failure of cactus-minigraph pipeline

  ComparativeGenomicsToolkit/cactus#2014 · Filter by author FerranLlobetC opened on Sep 20, 2026
  1

• Lower Giraffe Mapping Rate and Fewer SNPs Compared with BWA-GATK

  ComparativeGenomicsToolkit/cactus#1995 · Filter by author Sumit1331 opened on Sep 2, 2026
  1

• Uncertainty on graph edges?

  ComparativeGenomicsToolkit/cactus#1991 · Filter by author panosioannidis opened on Sep 1, 2026
  1

• Population-scale SV-GWAS design with minigraph-cactus + vg giraffe: are we missing a fundamental limitation for short-read cohorts?

  ComparativeGenomicsToolkit/cactus#1983 · Filter by author aaaniich opened on Aug 19, 2026
  1

• Advice on run time

  ComparativeGenomicsToolkit/cactus#1953 · Filter by author seynard opened on Jul 21, 2026
  2

• Advice on building a 500-genome pangenome with cactus-pangenome

  ComparativeGenomicsToolkit/cactus#1949 · Filter by author tudouzi1111 opened on Jul 9, 2026
  3

• error while running cactus-graphmap-join

  ComparativeGenomicsToolkit/cactus#1944 · Filter by author namitadube opened on Jun 3, 2026
  1

• Pre-filtering overlapping assembly contigs before Minigraph-Cactus

  ComparativeGenomicsToolkit/cactus#1943 · Filter by author hrluo93 opened on May 22, 2026
  2

• Strategies for highly heterozygous haplotype-resolved eukaryotic pangenomes with extreme structural variation

  ComparativeGenomicsToolkit/cactus#1937 · Filter by author GitEnricoNeko opened on May 14, 2026
  2

• Question about graph complexity and downstream suitability of Minigraph-Cactus graph for a haploid fungal species

  ComparativeGenomicsToolkit/cactus#1934 · Filter by author Sumit1331 opened on May 6, 2026
  1

• Error while running hal2maf

  ComparativeGenomicsToolkit/cactus#1925 · Filter by author josh3397 opened on Apr 23, 2026
  3

• Progressive cactus issue with --slurmArgs

  ComparativeGenomicsToolkit/cactus#1923 · Filter by author josh3397 opened on Apr 22, 2026
  2

• Changing the reference genome in minigraph_cactus run results in failed job - Job used more disk than requested

  ComparativeGenomicsToolkit/cactus#1922 · Filter by author evcurran opened on Apr 22, 2026
  1

• Haplotype input naming and using primary assembly as reference

  ComparativeGenomicsToolkit/cactus#1919 · Filter by author hrluo93 opened on Apr 15, 2026
  2

• clip_vg

  ComparativeGenomicsToolkit/cactus#1917 · Filter by author jwli-code opened on Apr 14, 2026
  7

• Question about interpreting ODGI chromosome visualization and zooming into variable regions

  ComparativeGenomicsToolkit/cactus#1916 · Filter by author Sumit1331 opened on Apr 14, 2026
  1

• cactus_consolidated OOM during BAR/abPOA phase with 16 genomes on 1 TB node

  ComparativeGenomicsToolkit/cactus#1914 · Filter by author Ruiqi-CUB opened on Apr 4, 2026
  1

• Using cactus to construct graph-pangenome across related species with different karyotypes / chromosome landscape

  ComparativeGenomicsToolkit/cactus#1911 · Filter by author WenjieUnizar opened on Mar 31, 2026
  2

• Error: Connection reset by peer

  ComparativeGenomicsToolkit/cactus#1909 · Filter by author covavara opened on Mar 27, 2026
  1

• vg index terminated with signal 15 during make_giraffe_indexes (dist index, ~1.4TB memory usage)

  ComparativeGenomicsToolkit/cactus#1903 · Filter by author shin0727 opened on Mar 3, 2026
  3

• How to restart an interrupted step-by-step task

  ComparativeGenomicsToolkit/cactus#1898 · Filter by author Blank921757 opened on Feb 14, 2026
  1

• cactus_sanitizeFastaHeaders fails: "Could not open input file" although Toil downloaded the fasta

  ComparativeGenomicsToolkit/cactus#1897 · Filter by author shin0727 opened on Feb 13, 2026
  4

• cactus-hal2maf: are regions on different scaffolds considered dupes?

  ComparativeGenomicsToolkit/cactus#1890 · Filter by author gwct opened on Feb 2, 2026
  1