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115 Commits

Author SHA1 Message Date
Heng Li
3c28777e7e Release minimap2-2.31 (r1302) 2026-05-19 18:39:04 -04:00
Heng Li
370f3f8236 add an alert about phishing 2025-09-09 11:23:09 -04:00
Heng Li
79c9cc186b Release minimap2-2.30 (r1287) 2025-06-15 17:54:11 -04:00
Heng Li
1fd85be6e2 Release minimap2-2.29 (r1283) 2025-04-18 13:41:47 -04:00
Heng Li
ff312a2957 documented 2-pass in README 2025-04-13 17:14:44 -04:00
Heng Li
75619c7b51 r1265: prefer spliced alignment 
mapq needs to be elevated
 2025-04-07 00:31:04 -04:00
Heng Li
d43f356ef9 fixed minor grammar issues 2025-04-06 18:35:46 -04:00
Heng Li
38acd6617f r1261: code clean up; renamed --jump-bed to -j 
Also added --pairing to replace --no-pairing and --pe-ind-chain
 2025-04-06 18:32:58 -04:00
Heng Li
dd90d9dde6 caution that the splice:sr is experimental 2025-04-04 16:34:40 -04:00
Heng Li
924fc4d671 minor 2025-04-02 13:06:03 -04:00
Heng Li
fc2d1e95b3 document splice:sr in README 2025-04-02 11:24:44 -04:00
Heng Li
8170693de3 Release minimap2-2.28 (r1209) 2024-03-27 10:57:17 -04:00
Heng Li
b6762503a9 Release minimap2-2.27 (r1193) 2024-03-12 13:20:07 -04:00
Aaron Darling
ace990c381 Illumina Complete Long Read presets (#1069) 
* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR

* Fix to enable use of general scoring matrix in ksw as suggested by lh3

---------

Co-authored-by: koadman <>
 2023-06-04 11:06:15 -04:00
Heng Li
e28a55be86 Release minimap2-2.26 (r1175) 2023-04-29 12:21:09 -04:00
Heng Li
4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Heng Li
e018caea32 added the second minimap2 paper 2022-03-01 11:05:09 -05:00
Heng Li
06fedaadd0 typo on simde 2021-12-26 15:38:06 -05:00
Heng Li
fe35e679e9 Release minimap2-2.24 (r1122) 2021-12-26 15:14:54 -05:00
Heng Li
d0cff3eb36 Release minimap2-2.23 (r1111) 2021-11-18 17:11:48 -05:00
Heng Li
7358a1ead1 Release minimap2-2.22 (r1101) 2021-08-07 11:30:31 -04:00
Heng Li
581f2d7123 Release minimap2-2.21 (r1071) 2021-07-06 13:18:55 -04:00
Torsten Houwaart
c83589b9ea Update README.md 
Clarification on approximate mapping
 2021-06-10 09:36:39 -04:00
Heng Li
ce7a59f412 Fixed a typo in README 
I just hate my butterfly keyboard!
 2021-05-27 15:43:04 -04:00
Heng Li
15471bd629 Release minimap2-2.20 (r1061) 2021-05-27 15:26:04 -04:00
Heng Li
ef09ccf104 Release minimap2-2.19 (r1055) 2021-05-26 21:01:03 -04:00
Ariel Erijman
cd66777bfb small typo 2021-05-23 13:09:55 -04:00
Heng Li
5d7d25e92d Merge remote-tracking branch 'origin/master' 2021-05-23 13:08:52 -04:00
Heng Li
2a3793bbd2 clarify that map-hifi is for HEAD only 
Resolves #747
 2021-05-23 13:08:15 -04:00
Cornelius Roemer
10502e2a78 Fixed typo in Readme.md 
deltion -> deletion
 2021-05-14 15:38:30 -04:00
Heng Li
42a11e1d58 Changed Travis to Github Actions in README 2021-05-10 12:58:25 -04:00
Heng Li
f7dc5799c5 clarify CLR when necessary 2021-05-01 15:56:33 -04:00
Heng Li
817cb81cb0 Updated README for the HiFi preset 2021-05-01 15:47:25 -04:00
Heng Li
b6ff332de1 Release minimap2-2.18 (r1015) 2021-04-09 13:33:34 -04:00
Heng Li
77abafaaf3 prepare for release 2021-04-09 13:18:56 -04:00
Heng Li
1c4b7e8a48 explained --junc-bed in README 2021-03-06 19:44:24 -05:00
Heng Li
ccb0f7b05d added a new Makefile for simde 2020-04-25 22:43:29 -04:00
mbrcic
3e16e4e39d Added documentation entry for added functionality, simde and no_simd. 2020-04-21 01:36:19 +02:00
Heng Li
5cb61f8ee6 added FAQ 2019-06-06 10:47:33 -04:00
Heng Li
7bc87b4175 Release minimap2-2.17 (r941) 2019-05-04 23:49:17 -04:00
Heng Li
6762368cf0 r940: added the splice:hq preset 
for high-quality CCS/mRNA splice alignment
 2019-05-04 14:00:31 -04:00
Heng Li
6b391e3373 Release minimap2-2.16 (r922) 2019-02-28 15:49:24 -05:00
Heng Li
ccf1680aaf make it explicit that -x is preferred for prebuilt 2019-02-27 12:43:33 -05:00
Heng Li
a8e1e3cbb8 updated citation with page numbers 2019-01-26 17:59:36 -05:00
Heng Li
c404f49569 Release minimap2-2.15 (r905) 2019-01-10 12:34:45 -05:00
Heng Li
59f23f7579 Release minimap2-2.14 (r883) 2018-11-06 00:03:16 -05:00
Heng Li
51e2abfa60 clarify that minimap2 may miss small exons 2018-10-22 11:16:16 -04:00
Heng Li
5d5d392c02 Release minimap2-2.13 (r850) 2018-10-11 13:18:31 -04:00
Heng Li
a5eafb75f9 Release minimap2-2.12 (r827) 2018-08-06 12:44:39 -04:00
Heng Li
8e606bcc06 added a -C5 example to Getting Started 2018-08-06 09:08:33 -04:00