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r179: changed the preset for assembly alignment

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Heng Li
2017-07-17 22:41:46 -04:00
parent 38aa66fa30
commit 941059292e
3 changed files with 20 additions and 6 deletions
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@@ -183,8 +183,14 @@ Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 -
.B map10k
PacBio/Oxford Nanopore read to reference mapping (-Hk19)
.TP
.B asm1m
Long assembly to reference mapping (-k19 -w19)
.B asm5
Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,61 -E2,1 -s200).
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%.
.TP
.B asm10
Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200). Up
to 10% sequence divergence.
.RE
.TP
.BI --max-chain-skip \ INT