Issues

• IndexError: list index out of range, sbatch/sacct error

  marbl/verkko#371 · Filter by author mkaterutter opened on Sep 26, 2026
  1

• Does verkko have plans to support minibwa?

  enhancement
  marbl/verkko#369 · Filter by author Fuwen-Wang opened on Sep 4, 2026
  1

  

• Segmentation fault in utgcns generateTemplateStitch() on massively collapsed repeat unitig (~94.4Mb, ~750K reads) during final HiC-phased consensus

  marbl/verkko#367 · Filter by author hanqu24 opened on Aug 21, 2026
  1

• 7-consensus error

  marbl/verkko#366 · Filter by author lyy005 opened on Aug 16, 2026
  5

• The --paths option can re-run the pipeline when initial asm or input file timestamps are updated

  marbl/verkko#308 · Filter by author skoren opened on Dec 11, 2024
  5

• 2 chromosomal fusions from verkko 2.2 assembly not supported by the data

  marbl/verkko#294 · Filter by author tbenavi1 opened on Oct 16, 2024
  11

• Questions related to interpretation results phased assembly.

  marbl/verkko#245 · Filter by author rfinkers opened on Apr 5, 2024
  54

  

• Better error reporting

  marbl/verkko#228 · Filter by author Dmitry-Antipov opened on Feb 1, 2024
  2

  

• Snakemake 8 compatibility

  enhancement
  marbl/verkko#224 · Filter by author tbenavi1 opened on Jan 13, 2024 · v2.3
  5

• Strange GFA outputs in uncompressed gfa

  marbl/verkko#199 · Filter by author skoren opened on Sep 28, 2023 · v2.3

• Homogenize trio vs hic architecture

  enhancement
  marbl/verkko#197 · Filter by author skoren opened on Sep 28, 2023 · v2.3
  2

• Hi-C plus Trio on same run

  enhancement
  marbl/verkko#193 · Filter by author Dmitry-Antipov opened on Sep 15, 2023 · v2.3
  2

  

• Likely incorrect ONT-based resolution

  marbl/verkko#190 · Filter by author skoren opened on Sep 12, 2023
  

• Potential graphaligner/resolution instability

  bug
  marbl/verkko#176 · Filter by author skoren opened on Jul 24, 2023
  3

  

• Improve coverage estimations for repeats

  marbl/verkko#172 · Filter by author Dmitry-Antipov opened on Jul 13, 2023

• Producing dual assemblies when no trio or Hi-C data is available

  enhancement
  marbl/verkko#157 · Filter by author smkumaill opened on Jun 16, 2023
  7

  

• Incorporate mer counting for haplotypes in verkko

  enhancement
  marbl/verkko#120 · Filter by author skoren opened on Jan 9, 2023 · v2.3
  

• Miscellaneous snakemake cleanup

  marbl/verkko#115 · Filter by author skoren opened on Nov 25, 2022
  1

  

• Consider multiplicities of original nodes in the final layout

  question
  marbl/verkko#13 · Filter by author snurk opened on Nov 13, 2021
  

• Consider alternate resolution in complex tangles

  enhancement
  marbl/verkko#5 · Filter by author skoren opened on Nov 5, 2021