From ee9f561e2fb661fcddf0c7ab308447b4af403e62 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 5 May 2019 09:30:56 -0400 Subject: [PATCH] Update the manpage to v2.17 --- minimap2.html | 32 ++++++++++++++++++++++++++------ 1 file changed, 26 insertions(+), 6 deletions(-) diff --git a/minimap2.html b/minimap2.html index b8d3251..c320acf 100644 --- a/minimap2.html +++ b/minimap2.html @@ -61,7 +61,7 @@ p { text-align: justify; } -minimap2.1 +Manual Page - minimap2(1)
@@ -437,6 +437,18 @@ on SIRV data, please add --splice-flank=no to the command line. +--junc-bed FILE   +Gene annotations in the BED12 format (aka 12-column BED), or intron positions +in 5-column BED. With this option, minimap2 prefers splicing in annotations. +BED12 file can be converted from GTF/GFF3 with ‘paftools.js gff2bed anno.gtf’ +[]. + + +--junc-bonus INT   +Score bonus for a splice donor or acceptor found in annotation (effective with +--junc-bed) [0]. + + --end-seed-pen INT   Drop a terminal anchor if s<log(g)+INT, where @@ -559,6 +571,10 @@ In PAF, output unmapped queries; the strand and the reference name fields are set to ‘*’. Warning: some paftools.js commands may not work with such output for the moment. + +--sam-hit-only   +In SAM, don’t output unmapped reads. + --version Print version number to stdout @@ -595,18 +611,18 @@ is determined by the sequencing error mode. asm5 Long assembly to reference mapping -(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100). Typically, the alignment will not extend to regions with 5% or higher sequence +(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50 --min-occ-floor=100). 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%. asm10 Long assembly to reference mapping -(-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 10% sequence divergence. +(-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50 --min-occ-floor=100). Up to 10% sequence divergence. asm20 Long assembly to reference mapping -(-k19 -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence. +(-k19 -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50 --min-occ-floor=100). Up to 20% sequence divergence. ava-pb @@ -621,12 +637,16 @@ Oxford Nanopore all-vs-all overlap mapping splice Long-read spliced alignment -(-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as +(-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the ‘N’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the ‘ms’ tag ignores introns to demote hits to pseudogenes. + +splice:hq   +Long-read splice alignment for PacBio CCS reads +(-xsplice -C5 -O6,24 -B4). sr Short single-end reads without splicing @@ -791,4 +811,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

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minimap2-2.16 (r922) minimap2 (1) 28 Feburary 2019
+
minimap2-2.17 (r941) minimap2 (1) 4 May 2019