@@ -437,6 +437,18 @@ on SIRV data, please add
--splice-flank=no to the command line.
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+--junc-bed FILE |
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+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 |
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+Score bonus for a splice donor or acceptor found in annotation (effective with
+--junc-bed) [0].
+ |
+|
--end-seed-pen INT |
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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.
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+|
+--sam-hit-only |
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+In SAM, don’t output unmapped reads.
+ |
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--version |
Print version number to stdout
@@ -595,18 +611,18 @@ is determined by the sequencing error mode.
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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%.
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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.
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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.
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ava-pb |
@@ -621,12 +637,16 @@ Oxford Nanopore all-vs-all overlap mapping
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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.
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+|
+splice:hq |
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+Long-read splice alignment for PacBio CCS reads
+(-xsplice -C5 -O6,24 -B4). |
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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).
- | minimap2-2.16 (r922) | minimap2 (1) | 28 Feburary 2019 |
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