mirror of
https://github.com/lh3/minimap2.git
synced 2026-10-01 02:18:12 +08:00
r518: increased the default -K to 500M
This helps multi-thread performance for ultra-long reads.
This commit is contained in:
+5
-10
@@ -1,4 +1,4 @@
|
||||
.TH minimap2 1 "20 September 2017" "minimap2-2.2 (r420)" "Bioinformatics tools"
|
||||
.TH minimap2 1 "17 October 2017" "minimap2-2.2-dirty (r518)" "Bioinformatics tools"
|
||||
.SH NAME
|
||||
.PP
|
||||
minimap2 - mapping and alignment between collections of DNA sequences
|
||||
@@ -263,18 +263,13 @@ thread may become the bottleneck. Apply this option to use one thread for input
|
||||
and another thread for output, at the cost of increased peak RAM.
|
||||
.TP
|
||||
.BI -K \ NUM
|
||||
Number of bases loaded into memory to process in a mini-batch [200M].
|
||||
Number of bases loaded into memory to process in a mini-batch [500M].
|
||||
Similar to option
|
||||
.BR -I ,
|
||||
K/M/G/k/m/g suffix is accepted. A large
|
||||
.I NUM
|
||||
helps load balancing in the multi-threading mode, at the cost of increased
|
||||
memory. Preset
|
||||
.B ava-pb
|
||||
and
|
||||
.B ava-ont
|
||||
use
|
||||
.BR -K500m .
|
||||
memory.
|
||||
.TP
|
||||
.B --version
|
||||
Print version number to stdout
|
||||
@@ -320,13 +315,13 @@ Up to 10% sequence divergence.
|
||||
.B ava-pb
|
||||
PacBio all-vs-all overlap mapping
|
||||
.RB ( -Hk19
|
||||
.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip
|
||||
.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
|
||||
.BR 25 ).
|
||||
.TP
|
||||
.B ava-ont
|
||||
Oxford Nanopore all-vs-all overlap mapping
|
||||
.RB ( -k15
|
||||
.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip
|
||||
.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
|
||||
.BR 25 ).
|
||||
Similarly, the major difference from
|
||||
.B ava-pb
|
||||
|
||||
Reference in New Issue
Block a user