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updated manpage

This commit is contained in:
Heng Li 2019-04-28 17:02:49 -04:00
parent e80759c97a
commit 2bb8cbbeef
1 changed files with 15 additions and 4 deletions
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minimap2.1
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@ -364,6 +364,17 @@ on SIRV data, please add
.B --splice-flank=no .B --splice-flank=no
to the command line. to the command line.
.TP .TP
.BR --junc-bed \ FILE
BED file consisting of annotated introns and their strands. With this option,
minimap2 prefers splicing in annotations.
.I FILE
can be generated with `paftools.js gff2bed -j ann.gtf' [].
.TP
.BR --junc-bonus \ INT
Score bonus for a splice donor or acceptor found in annotation (effective with
.BR --junc-bed )
[0].
.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 ,
@ -507,7 +518,7 @@ is determined by the sequencing error mode.
.B asm5 .B asm5
Long assembly to reference mapping Long assembly to reference mapping
.RB ( -k19 .RB ( -k19
.B -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 .B -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50
.BR --min-occ-floor=100 ). .BR --min-occ-floor=100 ).
Typically, the alignment will not extend to regions with 5% or higher sequence Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%. divergence. Only use this preset if the average divergence is far below 5%.
@ -515,14 +526,14 @@ divergence. Only use this preset if the average divergence is far below 5%.
.B asm10 .B asm10
Long assembly to reference mapping Long assembly to reference mapping
.RB ( -k19 .RB ( -k19
.B -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 .B -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50
.BR --min-occ-floor=100 ). .BR --min-occ-floor=100 ).
Up to 10% sequence divergence. Up to 10% sequence divergence.
.TP .TP
.B asm20 .B asm20
Long assembly to reference mapping Long assembly to reference mapping
.RB ( -k19 .RB ( -k19
.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 .B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50
.BR --min-occ-floor=100 ). .BR --min-occ-floor=100 ).
Up to 20% sequence divergence. Up to 20% sequence divergence.
.TP .TP
@ -544,7 +555,7 @@ is that this preset is not using HPC minimizers.
.B splice .B splice
Long-read spliced alignment Long-read spliced alignment
.RB ( -k15 .RB ( -k15
.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub .B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9
.BR --splice-flank=yes ). .BR --splice-flank=yes ).
In the splice mode, 1) long deletions are taken as introns and represented as In the splice mode, 1) long deletions are taken as introns and represented as
the the