Releases · lh3/minimap2
Minimap2-2.30 (r1287)Notable changes:
Improvement: consolidated --spsc.
Deprecation: subcommands splice2bed, gff2bed, gff2junc, junceval andexoneval in paftools.js are deprecated by minigff. They will remain
indefinitely for backward compatibility.
(2.30: 15 June 2025, r1287)
Minimap2-2.29 (r1283)Notable changes to minimap2:
New feature: added the splice:sr preset for short RNA-seq read alignment.
Users may use -j to specify known gene annotation to improve spliced
alignment close to the ends of short reads. Also added --write-junc and--pass1 for 2-pass short-read RNA-seq alignment.
Experimental feature: read splice scores from a file specified by --spsc
and consider the scores during base alignment. The feature makes it possible
to apply advanced splice models and to improve spliced alignment.
Change: adjusted the mapping quality calculation for spliced alignment.
Bugfixes: a) missing overlap alignment when base alignment is requested
(#969); b) incorrect summary information for long genomes (#1192); c)
missing parameter check for --score-N (#1226).
Improvement: a) warn about absent junction files (#1229); b) report an error
if a wrong preset prefixed with "splice" is specified (#589).
Notable changes to mappy:
Minimap2 now supports short/long genomic/RNA-seq read alignment along with
contig alignment and all-vs-all read overlapping. It produces identical genomic
long-read or contig alignment to v2.27. Short genomic read alignment and the
mapping quality of long RNA-seq read alignment may slightly differ in very rare
cases.
(2.29: 18 April 2025, r1283)
Minimap2-2.28 (r1209)Notable changes to minimap2:
Bugfix: --MD was not working properly due to the addition of --ds in the
last release (#1181 and #1182).
New feature: added an experimental preset lr:hqae for aligning accurate
long reads back to their assembly. It has been observed that map-hifi andlr:hq may produce many wrong alignments around centromeres when accurate
long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid
assembly constructed from them. This new preset produces much more accurate
alignment. It is still experimental and may be subjective to changes in
future.
Change: reduced the default --cap-kalloc to 500m to lower the peak
memory consumption (#855).
Notable changes to mappy:
Minimap2 should output identical alignments to v2.27.
(2.28: 27 March 2024, r1209)
Minimap2-2.27 (r1193)Notable changes to minimap2:
New feature: added the lr:hq preset for accurate long reads at ~1% error
rate. This was suggested by Oxford Nanopore developers (#1127). Whether
this preset works well for PacBio HiFi reads has not been tested.
New feature: added the map-iclr preset for Illumina Complete Long Reads
(#1069), provided by Illumina developers.
New feature: added option -b to specify mismatch penalty for base
transitions (i.e. A-to-G or C-to-T changes).
New feature: added option --ds to generate a new ds:Z tag that
indicates uncertainty in INDEL positions. It is an extension to cs. Themgutils-es6.js script in minigraph parses ds.
Bugfix: avoided a NULL pointer dereference (#1154). This would not have an
effect on most systems but would still be good to fix.
Bugfix: reverted the value of ms:i to pre-2.22 versions (#1146). This was
an oversight. See fcd4df2 for details.
Notable changes to paftools.js and mappy:
New feature: expose bw_long to mappy's Aligner class (#1124).
Bugfix: fixed several compatibility issues with k8 v1.0 (#1161 and #1166).
Subcommands "call", "pbsim2fq" and "mason2fq" were not working with v1.0.
Minimap2 should output identical alignments to v2.26, except the ms tag.
(2.27: 12 March 2024, r1193)
Minimap2-2.26 (r1175)Fixed the broken Python package. This is the only change.
(2.25: 25 April 2023, r1173)
Minimap2-2.25 (r1173)Notable changes:
Improvement: use the miniprot splice model for RNA-seq alignment by default.
This model considers non-GT-AG splice sites and has slightly higher
(<0.1%) accuracy and sensitivity on real human data.
Change: increased the default -I to 8G such that minimap2 would create a
uni-part index for a pair of mammalian genomes. This change may increase the
memory for all-vs-all read overlap alignment given large datasets.
New feature: output the sequences in secondary alignments with option--secondary-seq (#687).
Bugfix: --rmq was not parsed correctly (#1010)
Bugfix: possibly incorrect coordinate when applying end bonus to the target
sequence (#1025). This is a ksw2 bug. It does not affect minimap2 as
minimap2 is not using the affected feature.
Improvement: incorporated several changes for better compatibility with
Windows (#1051) and for minimap2 integration at Oxford Nanopore Technologies
(#1048 and #1033).
Improvement: output the HD-line in SAM output (#1019).
Improvement: check minimap2 index file in mappy to prevent segmentation
fault for certain indices (#1008).
For genomic sequences, minimap2 should give identical output to v2.24.
Long-read RNA-seq alignment may occasionally differ from previous versions.
(2.25: 25 April 2023, r1173)
Minimap2-2.24 (r1122)This release improves alignment around long poorly aligned regions. Older
minimap2 may chain through such regions in rare cases which may result in
missing alignments later. The issue has become worse since the the change of
the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
release provides a better solution with a X-drop-like heuristic and by enabling
two-bandwidth chaining in the assembly mode.
(2.24: 26 December 2021, r1122)
Minimap2-2.23 (r1111)Notable changes:
Bugfix: fixed missing alignments around long inversions (#806 and #816).
This bug affected v2.19 through v2.22.
Improvement: avoid extremely long mapping time for pathologic reads with
highly repeated k-mers not in the reference (#771). Use --q-occ-frac=0
to disable the new heuristic.
Change: use --cap-kalloc=1g by default.
(2.23: 18 November 2021, r1111)
Minimap2-2.22 (r1101)When choosing the best alignment, this release uses logarithm gap penalty and
query-specific mismatch penalty. It improves the sensitivity to long INDELs in
repetitive regions.
Other notable changes:
Bugfix: fixed an indirect memory leak that may waste a large amount of
memory given highly repetitive reference such as a 16S RNA database (#749).
All versions of minimap2 have this issue.
New feature: added --cap-kalloc to reduce the peak memory. This option is
not enabled by default but may become the default in future releases.
Known issue:
(2.22: 7 August 2021, r1101)
Minimap2-2.21 (r1071)This release fixed a regression in short-read mapping introduced in v2.19
(#776). It also fixed invalid comparisons of uninitialized variables, though
these do not affect final results (#752). Long-read alignment should be
identical to v2.20.
(2.21: 6 July 2021)
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