Issues

• Sequence causing segmentation fault

  lh3/minimap2#1359 · Filter by author guillaume-bugseq opened on Aug 4, 2026
  1

• missunderstanding of -p and -N options

  lh3/minimap2#1354 · Filter by author mariabernard opened on Jun 24, 2026

• mm_align1: Assertion `qs0 >= 0' failed on asm5 genome-to-genome alignment (-cx asm5)

  lh3/minimap2#1353 · Filter by author sarabehnamian opened on Jun 23, 2026

• High-MAPQ alignments are sometimes marked as supplementary to low-MAPQ primary alignments

  lh3/minimap2#1350 · Filter by author sjl opened on May 6, 2026

• Question- dRNA seq nanopore reads with polyA tail

  lh3/minimap2#1349 · Filter by author khushimamgain opened on Apr 1, 2026

• Unexpected soft-clipping when mapping to single chromosome reference

  lh3/minimap2#1342 · Filter by author guoshengkai123 opened on Jan 27, 2026

• Gap penalties check, options.c line 246

  enhancement
  lh3/minimap2#1337 · Filter by author lmjakt opened on Dec 3, 2025
  3

• Advice to increase the accuracy asked for mapping

  lh3/minimap2#1336 · Filter by author wdesaintjean opened on Nov 13, 2025

• some contigs have all MAPQ <5, some 60

  lh3/minimap2#1327 · Filter by author dcopetti opened on Oct 16, 2025

• Option to add header lines from string/file

  lh3/minimap2#1325 · Filter by author Stikus opened on Oct 7, 2025

• Phishing site : minimap2.com

  help wanted
  lh3/minimap2#1316 · Filter by author stefan-rooke opened on Sep 9, 2025
  8

• A corrupt FASTQ that causes minimap2 to create bogus SAM

  lh3/minimap2#1315 · Filter by author diekhans opened on Sep 6, 2025

• not properly aligned pair-end reads because of trimming

  lh3/minimap2#1307 · Filter by author korneel-emweb opened on Jul 1, 2025
  1

• paftools.js prints errors to stdout rather than stderr

  lh3/minimap2#1305 · Filter by author diekhans opened on Jun 20, 2025

• Minimap2 crashes for Wheat Scaffolding

  lh3/minimap2#1303 · Filter by author neupanebpn63 opened on Jun 9, 2025

• Enhancements for paired-end short-read RNAseq alignment

  feature-request
  lh3/minimap2#1297 · Filter by author JosephLalli opened on May 5, 2025
  3

• Query about Micro-C data usage

  lh3/minimap2#1295 · Filter by author NMaziak opened on Apr 23, 2025

• 1.9 TB is insufficient memory for whole genome alignment between two 5 GB genomes.

  lh3/minimap2#1272 · Filter by author altuffin opened on Jan 22, 2025
  3

• split reference genome alignment would be in consistence with aligning it as a whole?

  split-prefix
  lh3/minimap2#1270 · Filter by author Alipha-Clisa opened on Jan 13, 2025

• Mappy on MacOS arm_neon.h error

  lh3/minimap2#1235 · Filter by author christopher-vollmers opened on Aug 15, 2024
  3

• Question about different mappings of same read

  more info needed
  lh3/minimap2#1200 · Filter by author nadjano opened on Apr 24, 2024
  2

• Chaining score contributions from anchors seem to be capped by the anchor length, but the paper doesn't explain why

  question
  lh3/minimap2#1125 · Filter by author adamnovak opened on Oct 24, 2023
  2

• Order of operations in CIGAR

  enhancement
  lh3/minimap2#1118 · Filter by author baraaorabi opened on Sep 27, 2023
  4

• Single base exon in splice alignment

  lh3/minimap2#1099 · Filter by author baraaorabi opened on Aug 8, 2023
  1

• How to solve logic inconsistency?

  split-prefix
  lh3/minimap2#1084 · Filter by author Keltonc opened on Jul 9, 2023
  1