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Heng Li
2025-04-06 17:43:11 -04:00
parent 54a4718c9b
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.TH minimap2 1 "2 April 2025" "minimap2-2.28-dirty (r1248)" "Bioinformatics tools" .TH minimap2 1 "6 April 2025" "minimap2-2.28-dirty (r1259)" "Bioinformatics tools"
.SH NAME .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@@ -418,7 +418,7 @@ Penalty of a mismatch involving ambiguous bases [1].
.TP .TP
.BI --pe-ind-chain .BI --pe-ind-chain
For paired-end short reads, perform chaining for each end independently. For paired-end short reads, perform chaining for each end independently.
By default, minimap2 chains the two ends together. By default, minimap2 jointly chains the two ends.
.TP .TP
.BR --splice-flank = yes | no .BR --splice-flank = yes | no
Assume the next base to a Assume the next base to a
@@ -453,10 +453,13 @@ but not
.BR --junc-bed . .BR --junc-bed .
.TP .TP
.BR --junc-bed \ FILE .BR --junc-bed \ FILE
Gene annotations in the BED12 format (aka 12-column BED), or intron positions Junctions to prefer during base alignment.
in 5-column BED. With this option, minimap2 prefers splicing in annotations. .I FILE
BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf' can be gene annotations in the BED12 format (aka 12-column BED), or intron
[]. positions in 5-column BED. BED12 file can be converted from GTF/GFF3 with
`paftools.js gff2bed anno.gtf'. It is
.I NOT
recommended to apply this option for short RNA-seq reads. []
.TP .TP
.BR --junc-bonus \ INT .BR --junc-bonus \ INT
Score bonus for a splice donor or acceptor found in annotation [9]. Effective with Score bonus for a splice donor or acceptor found in annotation [9]. Effective with
@@ -464,6 +467,13 @@ Score bonus for a splice donor or acceptor found in annotation [9]. Effective wi
but not but not
.BR --spsc . .BR --spsc .
.TP .TP
.BR --jump-bed \ FILE
Junctions used to extend alignment towards ends of reads. Same format as with
.BR --junc-bed .
This option is intended for short RNA-seq reads, while
.B --junc-bed
for long noisy RNA-seq reads. []
.TP
.BI --end-seed-pen \ INT .BI --end-seed-pen \ INT
Drop a terminal anchor if Drop a terminal anchor if
.IR s <log( g )+ INT , .IR s <log( g )+ INT ,