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dev-r1078: decoupling ranking penalty

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Heng Li
2021-07-18 16:22:48 -04:00
parent 15118dd521
commit 8a6edab847
5 changed files with 23 additions and 17 deletions
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@@ -573,7 +573,7 @@ Up to 20% sequence divergence.
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
.BR --splice-flank=yes ).
In the splice mode, 1) long deletions are taken as introns and represented as
the
@@ -592,7 +592,7 @@ Long-read splice alignment for PacBio CCS reads
.B sr
Short single-end reads without splicing
.RB ( -k21
.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
.B -s40 -g100 -2K50m --heap-sort=yes
.BR --secondary=no ).
.TP