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missunderstanding of -p and -N options

Status: Open.

#1354 In lh3/minimap2;

· mariabernard opened on Jun 24, 2026

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

Status: Open.

#1353 In lh3/minimap2;

· sarabehnamian opened on Jun 23, 2026

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

Status: Open.

#1350 In lh3/minimap2;

· sjl opened on May 6, 2026

Question- dRNA seq nanopore reads with polyA tail

Status: Open.

#1349 In lh3/minimap2;

· khushimamgain opened on Apr 1, 2026

Unexpected soft-clipping when mapping to single chromosome reference

Status: Open.

#1342 In lh3/minimap2;

· guoshengkai123 opened on Jan 27, 2026

Gap penalties check, options.c line 246

enhancement

Status: Open.

#1337 In lh3/minimap2;

· lmjakt opened on Dec 3, 2025

Advice to increase the accuracy asked for mapping

Status: Open.

#1336 In lh3/minimap2;

· wdesaintjean opened on Nov 13, 2025

some contigs have all MAPQ <5, some 60

Status: Open.

#1327 In lh3/minimap2;

· dcopetti opened on Oct 16, 2025

Option to add header lines from string/file

Status: Open.

#1325 In lh3/minimap2;

· Stikus opened on Oct 7, 2025

Phishing site : minimap2.com

help wanted

Status: Open.

#1316 In lh3/minimap2;

· stefan-rooke opened on Sep 9, 2025

A corrupt FASTQ that causes minimap2 to create bogus SAM

Status: Open.

#1315 In lh3/minimap2;

· diekhans opened on Sep 6, 2025

not properly aligned pair-end reads because of trimming

Status: Open.

#1307 In lh3/minimap2;

· korneel-emweb opened on Jul 1, 2025