Issues

• assertion failed: n_codes < SIZE How many mods does modkit support?

  nanoporetech/modkit#728 · Filter by author lpryszcz opened on Oct 16, 2026

• modkit-0.6.4 :: help misses some Commands description

  nanoporetech/modkit#727 · Filter by author EricDeveaud opened on Oct 13, 2026
  2

• modkit (0.6.4) pileup - Segmentation fault

  nanoporetech/modkit#726 · Filter by author mfurla opened on Oct 12, 2026

• Report modifications only matching cannonical reference base

  nanoporetech/modkit#725 · Filter by author lpryszcz opened on Oct 2, 2026

• modkit probability threshold

  nanoporetech/modkit#723 · Filter by author ArgAntonia opened on Sep 18, 2026

• dmr pair region output has effect_size sign inverted relative to the documentation and to single-site output

  nanoporetech/modkit#721 · Filter by author mileskatahdin opened on Sep 9, 2026
  3

• pileup: worker panic (base_mods_adapter.rs:80 "entered unreachable code") is silently swallowed in whole-genome mode — presents as an infinite zero-CPU hang

  nanoporetech/modkit#719 · Filter by author eelkebos opened on Aug 25, 2026

• Question regarding region-based DMR analysis

  nanoporetech/modkit#718 · Filter by author tinatucci opened on Aug 25, 2026

• Bug in modkit v0.6.4："fail" column in "modkit extract calls" output may use MM tag when matching --filter-threshold, G-h and G-m are not recognized as C

  bugtroubleshooting
  nanoporetech/modkit#717 · Filter by author jinglicharles-pixel opened on Aug 23, 2026
  3

• Effect of unequal coverage and lack of biological replicates on global 6mA comparisons

  nanoporetech/modkit#716 · Filter by author angelluigi opened on Aug 20, 2026

• Bug in modkit extract full, canonical_base does not match reference sequence

  nanoporetech/modkit#715 · Filter by author awjga opened on Aug 19, 2026

• Modkit extract calls: 5hmC ("h") calls correspond mostly to <50% Mod_qual from modkit extract full

  nanoporetech/modkit#646 · Filter by author ahong017 opened on Aug 3, 2026

• Question regarding N1-methylpseudouridine detection support

  question
  nanoporetech/modkit#645 · Filter by author Seongmin-Jang-1165 opened on Aug 3, 2026
  1

• Bug in modkit pileup with --combine-mods v0.6.4

  bugbuild-available
  nanoporetech/modkit#644 · Filter by author SchwarzMarek opened on Jul 30, 2026
  4

• max-depth and high-depth options

  question
  nanoporetech/modkit#643 · Filter by author SchwarzMarek opened on Jul 27, 2026
  1

• Abnormal color gradient observed when plotting using the dmr isoform command

  troubleshooting
  nanoporetech/modkit#642 · Filter by author rain-zjg opened on Jul 27, 2026
  2

• Does modkit sample-probs still have an option for only mapped regions?

  build-availablequestion
  nanoporetech/modkit#641 · Filter by author MafaldaSoares opened on Jul 22, 2026
  2

• modkit (V0.6.4 )pileup hangs mid-run (process alive, 0% CPU) on large metagenomic BAM

  troubleshooting
  nanoporetech/modkit#640 · Filter by author ran525 opened on Jul 18, 2026
  10

• High 6mA threshold in epi2me chromatin accessibility dataset

  Analysis Question
  nanoporetech/modkit#639 · Filter by author billytcl opened on Jul 1, 2026
  8

• modkit pileup --phased return only combined haplotype while processing whole genome

  troubleshooting
  nanoporetech/modkit#638 · Filter by author JbaptisteLam opened on Jun 19, 2026
  2

• Does --single-code h perform 5hmC-vs-all or 5hmC-only DMR analysis?

  documentation
  nanoporetech/modkit#637 · Filter by author danammak opened on Jun 17, 2026
  4

• Multi-gpu processing on tch branch of Modkit

  nanoporetech/modkit#634 · Filter by author adbeggs opened on Jun 11, 2026
  1

• compare-tx-sites multiple replicates per condition

  enhancement
  nanoporetech/modkit#633 · Filter by author marcellogiunta opened on Jun 4, 2026
  11

• Explanation for modkit stats output

  question
  nanoporetech/modkit#631 · Filter by author dietvin opened on Jun 3, 2026
  1

• modkit v0.6.3 error when running on remora generated modbam

  enhancement
  nanoporetech/modkit#630 · Filter by author samim21 opened on Jun 2, 2026
  3