Release minimap2-2.19 (r1055)

NEWS.md

@@ -1,3 +1,42 @@
+Release 2.19-r1055 (26 May 2021)
+--------------------------------
+
+This release includes a few important improvements backported from unimap:
+
+ * Improvement: more contiguous alignment through long INDELs. This is enabled
+   by the minigraph chaining algorithm. All `asm*` presets now use the new
+   algorithm. They can find INDELs up to 100kb and may be faster for
+   chromosome-long contigs. The default mode and `map*` presets use this
+   algorithm to replace the long-join heuristic.
+
+ * Improvement: better alignment in highly repetitive regions by rescuing
+   high-occurrence seeds. If the distance between two adjacent seeds is too
+   large, attempt to choose a fraction of high-occurrence seeds in-between.
+   Minimap2 now produces fewer clippings and alignment break points in long
+   satellite regions.
+
+ * Improvement: allow to specify an interval of k-mer occurrences with `-U`.
+   For repeat-rich genomes, the automatic k-mer occurrence threshold determined
+   by `-f` may be too large and makes alignment impractically slow. The new
+   option protects against such cases. Enabled for `asm*` and `map-hifi`.
+
+ * New feature: added the `map-hifi` preset for maping PacBio High-Fidelity
+   (HiFi) reads.
+
+ * Change to the default: apply `--cap-sw-mem=100m` for genomic alignment.
+
+ * Bugfix: minimap2 could not generate an index file with `-xsr` (#734).
+
+This release represents the most signficant algorithmic change since v2.1 in
+2017. With features backported from unimap, minimap2 now has similar power to
+unimap for contig alignment. Unimap will remain an experimental project and is
+no longer recommended over minimap2. Sorry for reverting the recommendation in
+short time.
+
+(2.20: 26 May 2021, r1055)
+
+
+
 Release 2.18-r1015 (9 April 2021)
 ---------------------------------
 

README.md

@@ -14,8 +14,8 @@ cd minimap2 && make
 # use presets (no test data)
 ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio CLR genomic reads
 ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
-./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18)
-./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (GitHub HEAD)
+./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or lateer)
+./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18 or earlier)
 ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
 ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
 ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore Direct RNA-seq
@@ -27,9 +27,6 @@ cd minimap2 && make
 # man page for detailed command line options
 man ./minimap2.1
 ```
-[Unimap][unimap] is recommended for aligning long contigs against a reference
-genome. It often takes less wall-clock time and is much more sensitive to long
-insertions and deletions.
 
 ## Table of Contents
 
@@ -77,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.18/minimap2-2.18_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.18_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.19_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code

cookbook.md

@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.18/minimap2-2.18_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.18_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.19_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -

main.c

@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.18-r1054-dirty"
+#define MM_VERSION "2.19-r1055"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "9 April 2021" "minimap2-2.18 (r1015)" "Bioinformatics tools"
+.TH minimap2 1 "26 May 2021" "minimap2-2.19 (r1055)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.18-r1053-dirty';
+var paftools_version = '2.19-r1055';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.18'
+__version__ = '2.19'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.18',
+	version = '2.19',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),