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Cutoff Threshold Sensitivity in Human Samples

Status: Open.

#616 In nanoporetech/modkit;

· JRenGit opened on May 6, 2026

v0.6.2 tag contains Cargo.toml with version 0.6.1 — binary self-reports wrong version

Status: Open.

#614 In nanoporetech/modkit;

· SuhasSrinivasan opened on May 4, 2026

V0.6.1 does not work on pacbio samples, while v0.5.0 worked fine (no problems with ONT)

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#612 In nanoporetech/modkit;

· AmberVerhasselt opened on Apr 22, 2026

estimated pass threshold with default settings very high (v0.5.0 and v.0.6.1)

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#611 In nanoporetech/modkit;

· AmberVerhasselt opened on Apr 15, 2026

pileup CLI parse failure

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#609 In nanoporetech/modkit;

· aadali opened on Apr 10, 2026

Modkit pileup - segmentation fault and performance issues in high-coverage regions

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#607 In nanoporetech/modkit;

· mfurla opened on Apr 7, 2026

Discrepancy in calls when running individual modified base pileup and combined modbase pileup

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#606 In nanoporetech/modkit;

· gsukrit opened on Apr 7, 2026

modkit pileup --include-bed silently rejects BED4 files, produces zero valid positions with no warning

bugSomething isn't workingSomething isn't working

Status: Open.

#605 In nanoporetech/modkit;

· sahuno opened on Apr 6, 2026

Invalid data for modkit dmr pair

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#604 In nanoporetech/modkit;

· caballero opened on Apr 1, 2026

Question about DMR pair results

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#603 In nanoporetech/modkit;

· AlvinTam-lab opened on Mar 31, 2026

Can I use modkit pileup on newly identified insertions from ONT reads?

enhancementNew feature or requestNew feature or request

Status: Open.

#602 In nanoporetech/modkit;

· msfalmeida opened on Mar 26, 2026

Please provide a script to compile modkit for macOS

Status: Open.

#600 In nanoporetech/modkit;

· SuhasSrinivasan opened on Mar 23, 2026