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r1118: use -r1k,100k for asm* modes

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Heng Li
2021-12-23 20:43:54 -05:00
parent c8f0a35c40
commit d3a89d34d4
3 changed files with 5 additions and 5 deletions
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minimap2.1
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@@ -565,7 +565,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome
.B asm5
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
.BR -N50 ).
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%.
@@ -573,14 +573,14 @@ divergence. Only use this preset if the average divergence is far below 5%.
.B asm10
Long assembly to reference mapping
.RB ( -k19
.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
.BR -N50 ).
Up to 10% sequence divergence.
.TP
.B asm20
Long assembly to reference mapping
.RB ( -k19
.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.BR -N50 ).
Up to 20% sequence divergence.
.TP