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r1052: default -g to 5k

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Heng Li
2021-05-24 16:46:16 -04:00
parent 34a41197d7
commit 41d7ccb191
3 changed files with 11 additions and 13 deletions
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minimap2.1
+7 -11
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@@ -165,8 +165,8 @@ Stop chain enlongation if there are no minimizers within
.IR NUM -bp
[10k].
.TP
.BI -r \ INT
Bandwidth used in chaining and DP-based alignment [500]. This option
.BI -r \ NUM
Bandwidth used in chaining and DP-based alignment [500,20k]. This option
approximately controls the maximum gap size.
.TP
.BI -n \ INT
@@ -279,10 +279,6 @@ Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by
.BR -r .
.TP
.BI --lj-min-ratio \ FLOAT
Fraction of query sequence length required to bridge a long gap [0.5]. A
smaller value helps to recover longer gaps, at the cost of more false gaps.
.TP
.B --splice
Enable the splice alignment mode.
.TP
@@ -542,7 +538,7 @@ default mode.
.B map-hifi
Align PacBio high-fidelity (HiFi) reads to a reference genome
.RB ( -k19
.B -w19 -U50,500 -A1 -B4 -O6,26 -E2,1
.B -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1
.BR -s200 ).
.TP
.B map-pb
@@ -552,7 +548,7 @@ 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 --no-long-join -A1 -B19 -O39,81 -E3,1 -s200 -z200
.B -w19 -U50,500 --rmq -r100k -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%.
@@ -560,21 +556,21 @@ 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 --no-long-join -A1 -B9 -O16,41 -E2,1 -s200 -z200
.B -w19 -U50,500 --rmq -r100k -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 --no-long-join -A1 -B4 -O6,26 -E2,1 -s200 -z200
.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
.BR -N50 ).
Up to 20% sequence divergence.
.TP
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2000 -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 -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