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miniprot-like splice model

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slightly worse on iso-seq and slightly better on direct-RNA
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Heng Li
2022-10-06 09:10:17 -04:00
parent 5aa4355ca8
commit 6c2cbf7903
7 changed files with 104 additions and 7 deletions
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minimap2.1
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@@ -588,7 +588,7 @@ Up to 20% sequence divergence.
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -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