Update minimap2

bio/json/minimap2.json

@@ -1 +1 @@
-{"name":"minimap2","description":"minimap2","usage":"minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]","options":[{"names":["-x"],"argument":"{map-pb|map_ont|map-hifi|ava-pb|ava-ont|asm5|asm10|asm20|splice|splice:hg|sr}","description":"preset (always applied before other options; see minimap2.1 for details) []"},{"names":["-H"],"argument":"","description":"use homopolymer-compressed k-mer (preferrable for PacBio)"},{"names":["-k"],"argument":"INT","description":"k-mer size (no larger than 28) [15]"},{"names":["-w"],"argument":"INT","description":"minimizer window size [10]"},{"names":["-I"],"argument":"NUM","description":"split index for every ~NUM input bases [4G]"},{"names":["-d"],"argument":"FILE","description":"dump index to FILE []"},{"names":["-f"],"argument":"FLOAT","description":"filter out top FLOAT fraction of repetitive minimizers [0.0002]"},{"names":["-g"],"argument":"NUM","description":"stop chain enlongation if there are no minimizers in INT-bp [5000]"},{"names":["-G"],"argument":"NUM","description":"max intron length (effective with -xsplice; changing -r) [200k]"},{"names":["-F"],"argument":"NUM","description":"max fragment length (effective with -xsr or in the fragment mode) [800]"},{"names":["-r"],"argument":"NUM[,NUM]","description":"chaining/alignment bandwidth and long-join bandwidth [500,20000]"},{"names":["-n"],"argument":"INT","description":"minimal number of minimizers on a chain [3]"},{"names":["-m"],"argument":"INT","description":"minimal chaining score (matching bases minus log gap penalty) [40]"},{"names":["-X"],"argument":"","description":"skip self and dual mappings (for the all-vs-all mode)"},{"names":["-p"],"argument":"FLOAT","description":"min secondary-to-primary score ratio [0.8]"},{"names":["-N"],"argument":"INT","description":"retain at most INT secondary alignments [5]"},{"names":["-A"],"argument":"INT","description":"matching score [2]"},{"names":["-B"],"argument":"INT","description":"mismatch penalty [4]"},{"names":["-O"],"argument":"INT[,INT]","description":"gap open penalty [4,24]"},{"names":["-E"],"argument":"INT[,INT]","description":"gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1]"},{"names":["-z"],"argument":"INT[,INT]","description":"Z-drop score and inversion Z-drop score [400,200]"},{"names":["-s"],"argument":"INT","description":"minimal peak DP alignment score [80]"},{"names":["-u"],"argument":"CHAR","description":"how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]"},{"names":["-a"],"argument":"","description":"output in the SAM format (PAF by default)"},{"names":["-o"],"argument":"FILE","description":"output alignments to FILE [stdout]"},{"names":["-L"],"argument":"","description":"write CIGAR with >65535 ops at the CG tag"},{"names":["-R"],"argument":"STR","description":"SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []"},{"names":["-c"],"argument":"","description":"output CIGAR in PAF"},{"names":["--cs"],"argument":"[=STR]","description":"output the cs tag; STR is 'short' (if absent) or 'long' [none]"},{"names":["--MD"],"argument":"","description":"output the MD tag"},{"names":["--eqx"],"argument":"","description":"write =/X CIGAR operators"},{"names":["-Y"],"argument":"","description":"use soft clipping for supplementary alignments"},{"names":["-t"],"argument":"INT","description":"number of threads [3]"},{"names":["-K"],"argument":"NUM","description":"minibatch size for mapping [500M]"},{"names":["--version"],"argument":"","description":"show version number"}],"version":"2.24-r1122","tldr":"> Map and align between collections of DNA sequences.\n> More information: <https://lh3.github.io/minimap2/>.\n\n- Get alignment in SAM format\n\n`minimap2 -a {{ref.fa}} {{query.fq}} > {{alignment.sam}}`\n\n- Map long noisy genomic reads (PacBio):\n\n`minimap2 -ax map-pb {{ref.fa}} {{pacbio-reads.fq}} > {{aln.sam}}`\n\n- Map long cDNA-seq reads (Oxford Nanopore):\n\n`minimap2 -ax splice {{ref.fa}} {{nanopore-cdna.fa}} > {{aln.sam}}`\n\n- Find overlaps between long reads (Oxford Nanopore):\n\n`minimap2 -x ava-ont {{reads.fq}} {{reads.fq}} > {{ovlp.paf}}`\n\n- Map short accurate paired-end genomic reads:\n\n`minimap2 -ax sr {{ref.fa}} {{read1.fq}} {{read2.fq}} > s{{aln.sam}}`\n\n- Full genome/assembly alignment:\n\n`minimap2 -ax asm5 {{ref.fa}} {{asm.fa}} > {{aln.sam}}`\n"}
+{"name":"minimap2","description":"minimap2","usage":"minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]","options":[{"names":["-x"],"argument":"{map-ont|lr:hq|map-hifi|map-pb|map-iclr|asm5|asm10|asm20|splice|splice:hg|sr|ava-pb|ava-ont}","description":"preset (always applied before other options; see minimap2.1 for details) []"},{"names":["-H"],"argument":"","description":"use homopolymer-compressed k-mer (preferrable for PacBio)"},{"names":["-k"],"argument":"INT","description":"k-mer size (no larger than 28) [15]"},{"names":["-w"],"argument":"INT","description":"minimizer window size [10]"},{"names":["-I"],"argument":"NUM","description":"split index for every ~NUM input bases [8G]"},{"names":["-d"],"argument":"FILE","description":"dump index to FILE []"},{"names":["-f"],"argument":"FLOAT","description":"filter out top FLOAT fraction of repetitive minimizers [0.0002]"},{"names":["-g"],"argument":"NUM","description":"stop chain enlongation if there are no minimizers in INT-bp [5000]"},{"names":["-G"],"argument":"NUM","description":"max intron length (effective with -xsplice; changing -r) [200k]"},{"names":["-F"],"argument":"NUM","description":"max fragment length (effective with -xsr or in the fragment mode) [800]"},{"names":["-r"],"argument":"NUM[,NUM]","description":"chaining/alignment bandwidth and long-join bandwidth [500,20000]"},{"names":["-n"],"argument":"INT","description":"minimal number of minimizers on a chain [3]"},{"names":["-m"],"argument":"INT","description":"minimal chaining score (matching bases minus log gap penalty) [40]"},{"names":["-X"],"argument":"","description":"skip self and dual mappings (for the all-vs-all mode)"},{"names":["-p"],"argument":"FLOAT","description":"min secondary-to-primary score ratio [0.8]"},{"names":["-N"],"argument":"INT","description":"retain at most INT secondary alignments [5]"},{"names":["-A"],"argument":"INT","description":"matching score [2]"},{"names":["-B"],"argument":"INT","description":"mismatch penalty (larger value for lower divergence) [4]"},{"names":["-O"],"argument":"INT[,INT]","description":"gap open penalty [4,24]"},{"names":["-E"],"argument":"INT[,INT]","description":"gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1]"},{"names":["-z"],"argument":"INT[,INT]","description":"Z-drop score and inversion Z-drop score [400,200]"},{"names":["-s"],"argument":"INT","description":"minimal peak DP alignment score [80]"},{"names":["-u"],"argument":"CHAR","description":"how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]"},{"names":["-J"],"argument":"INT","description":"splice mode. 0: original minimap2 model; 1: miniprot model [1]"},{"names":["-a"],"argument":"","description":"output in the SAM format (PAF by default)"},{"names":["-o"],"argument":"FILE","description":"output alignments to FILE [stdout]"},{"names":["-L"],"argument":"","description":"write CIGAR with >65535 ops at the CG tag"},{"names":["-R"],"argument":"STR","description":"SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []"},{"names":["-c"],"argument":"","description":"output CIGAR in PAF"},{"names":["--cs"],"argument":"[=STR]","description":"output the cs tag; STR is 'short' (if absent) or 'long' [none]"},{"names":["--ds"],"argument":"","description":"output the ds tag, which is an extension to cs"},{"names":["--MD"],"argument":"","description":"output the MD tag"},{"names":["--eqx"],"argument":"","description":"write =/X CIGAR operators"},{"names":["-Y"],"argument":"","description":"use soft clipping for supplementary alignments"},{"names":["-t"],"argument":"INT","description":"number of threads [3]"},{"names":["-K"],"argument":"NUM","description":"minibatch size for mapping [500M]"},{"names":["--version"],"argument":"","description":"show version number"}],"version":"2.28-r1209","tldr":"> Map and align between collections of DNA sequences.\n> More information: <https://lh3.github.io/minimap2/>.\n\n- Get alignment in SAM format\n\n`minimap2 -a {{ref.fa}} {{query.fq}} > {{alignment.sam}}`\n\n- Map long noisy genomic reads (PacBio):\n\n`minimap2 -ax map-pb {{ref.fa}} {{pacbio-reads.fq}} > {{aln.sam}}`\n\n- Map long cDNA-seq reads (Oxford Nanopore):\n\n`minimap2 -ax splice {{ref.fa}} {{nanopore-cdna.fa}} > {{aln.sam}}`\n\n- Find overlaps between long reads (Oxford Nanopore):\n\n`minimap2 -x ava-ont {{reads.fq}} {{reads.fq}} > {{ovlp.paf}}`\n\n- Map short accurate paired-end genomic reads:\n\n`minimap2 -ax sr {{ref.fa}} {{read1.fq}} {{read2.fq}} > s{{aln.sam}}`\n\n- Full genome/assembly alignment:\n\n`minimap2 -ax asm5 {{ref.fa}} {{asm.fa}} > {{aln.sam}}`\n"}

bio/yaml/minimap2.yaml

@@ -4,7 +4,7 @@ usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]
 options:
   - names:
       - -x
-    argument: '{map-pb|map_ont|map-hifi|ava-pb|ava-ont|asm5|asm10|asm20|splice|splice:hg|sr}'
+    argument: '{map-ont|lr:hq|map-hifi|map-pb|map-iclr|asm5|asm10|asm20|splice|splice:hg|sr|ava-pb|ava-ont}'
     description: preset (always applied before other options; see minimap2.1 for details) []
   - names:
       - -H
@@ -21,7 +21,7 @@ options:
   - names:
       - -I
     argument: NUM
-    description: split index for every ~NUM input bases [4G]
+    description: split index for every ~NUM input bases [8G]
   - names:
       - -d
     argument: FILE
@@ -73,7 +73,7 @@ options:
   - names:
       - -B
     argument: INT
-    description: mismatch penalty [4]
+    description: mismatch penalty (larger value for lower divergence) [4]
   - names:
       - -O
     argument: INT[,INT]
@@ -94,6 +94,10 @@ options:
       - -u
     argument: CHAR
     description: how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]
+  - names:
+      - -J
+    argument: INT
+    description: 'splice mode. 0: original minimap2 model; 1: miniprot model [1]'
   - names:
       - -a
     argument: ""
@@ -118,6 +122,10 @@ options:
       - --cs
     argument: '[=STR]'
     description: output the cs tag; STR is 'short' (if absent) or 'long' [none]
+  - names:
+      - --ds
+    argument: ""
+    description: output the ds tag, which is an extension to cs
   - names:
       - --MD
     argument: ""
@@ -142,7 +150,7 @@ options:
       - --version
     argument: ""
     description: show version number
-version: 2.24-r1122
+version: 2.28-r1209
 tldr: |
   > Map and align between collections of DNA sequences.
   > More information: <https://lh3.github.io/minimap2/>.