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r172: separated PacBio and ONT read overlapping 

HPC k-mer works better for PacBio, but worse for ONT. Interesting...
This commit is contained in:
Heng Li 2017-07-11 15:12:35 -04:00
parent 7598809577
commit cfa083a98b
2 changed files with 15 additions and 7 deletions
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11
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r171-pre"
#define MM_VERSION "2.0-r172-pre"
void liftrlimit()
{
@ -122,7 +122,11 @@ int main(int argc, char *argv[])
if (c == 'I') batch_size = (uint64_t)(x + .499);
else minibatch_size = (uint64_t)(x + .499);
} else if (c == 'x') {
if (strcmp(optarg, "ava10k") == 0) {
if (strcmp(optarg, "ava-ont") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000;
k = 15, w = 5;
} else if (strcmp(optarg, "ava-pb") == 0) {
opt.flag |= MM_F_AVA | MM_F_NO_SELF;
opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000;
is_hpc = 1, k = 19, w = 5;
@ -159,7 +163,8 @@ int main(int argc, char *argv[])
fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
fprintf(stderr, " -D FLOAT min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
fprintf(stderr, " ava10k: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio/ONT all-vs-all read mapping)\n");
fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio read overlap)\n");
fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 (ONT read overlap)\n");
fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " Alignment:\n");

11
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "8 July 2017" "minimap2-2.0-r160-pre" "Bioinformatics tools"
.TH minimap2 1 "11 July 2017" "minimap2-2.0-r172-pre" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -54,7 +54,7 @@ minimap2
.RS 4
minimap2
.B -x
ava10k
ava-ont
.RB [ -t
.IR nThreads ]
.I target.fa
@ -180,8 +180,11 @@ Available
are:
.RS
.TP 8
.B ava10k
PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05)
.B ava-pb
PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05 -g10000)
.TP 8
.B ava-ont
Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -D.05 -g10000)
.TP
.B map10k
PacBio/Oxford Nanopore read to reference mapping (-Hk19)