r518: increased the default -K to 500M

This helps multi-thread performance for ultra-long reads.
This commit is contained in:
Heng Li
2017-10-17 13:21:29 -04:00
parent 25ffd72690
commit 04cf4ebf5e
3 changed files with 10 additions and 17 deletions
+5 -10
View File
@@ -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