r190: default -k to 15; added -x map-ont
This commit is contained in:
Heng Li
parent
470021fd27
commit
4aff301ef4
22
main.c
22
main.c
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@ -10,7 +10,7 @@
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#include "minimap.h"
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#include "mmpriv.h"
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#define MM_VERSION "2.0-r189-dirty"
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#define MM_VERSION "2.0-r190-dirty"
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void liftrlimit()
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{
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@ -63,7 +63,7 @@ static struct option long_options[] = {
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int main(int argc, char *argv[])
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{
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mm_mapopt_t opt;
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int i, c, k = 17, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
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int i, c, k = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx;
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int minibatch_size = 200000000;
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uint64_t batch_size = 4000000000ULL;
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mm_bseq_file_t *fp = 0;
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@ -135,8 +135,10 @@ int main(int argc, char *argv[])
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opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.max_gap = 10000, opt.max_chain_skip = 25;
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minibatch_size = 500000000;
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is_hpc = 1, k = 19, w = 5;
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} else if (strcmp(optarg, "map10k") == 0) {
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} else if (strcmp(optarg, "map10k") == 0 || strcmp(optarg, "map-pb") == 0) {
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is_hpc = 1, k = 19;
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} else if (strcmp(optarg, "map-ont") == 0) {
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is_hpc = 0, k = 15;
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} else if (strcmp(optarg, "asm5") == 0) {
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k = 19, w = 19;
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opt.a = 1, opt.b = 19, opt.q = 39, opt.q2 = 81, opt.e = 3, opt.e2 = 1, opt.zdrop = 200;
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@ -172,12 +174,6 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -X skip self and dual mappings (for the all-vs-all mode)\n");
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fprintf(stderr, " -p FLOAT min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
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fprintf(stderr, " -N INT retain at most INT secondary alignments [%d]\n", opt.best_n);
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fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
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fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
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fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
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fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
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fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
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fprintf(stderr, " Alignment:\n");
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fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
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fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);
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@ -193,6 +189,14 @@ int main(int argc, char *argv[])
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fprintf(stderr, " -K NUM minibatch size [200M]\n");
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// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);
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fprintf(stderr, " -V show version number\n");
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fprintf(stderr, " Preset:\n");
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fprintf(stderr, " -x STR preset (recommended to be applied before other options) []\n");
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fprintf(stderr, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");
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fprintf(stderr, " map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\n");
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fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
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fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
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fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
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fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
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fprintf(stderr, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
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return 1;
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}
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78
minimap2.1
78
minimap2.1
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@ -1,4 +1,4 @@
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.TH minimap2 1 "18 July 2017" "minimap2-2.0-r180-dirty" "Bioinformatics tools"
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.TH minimap2 1 "19 July 2017" "minimap2-2.0-r190-dirty" "Bioinformatics tools"
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.SH NAME
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.PP
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minimap2 - mapping and alignment between collections of DNA sequences
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@ -74,7 +74,7 @@ SAM format.
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.SS Indexing options
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.TP 10
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.BI -k \ INT
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Minimizer k-mer length [17]
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Minimizer k-mer length [15]
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.TP
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.BI -w \ INT
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Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
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@ -164,35 +164,6 @@ secondary alignments [5]. This option has no effect when
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.B -X
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is applied.
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.TP
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.BI -x \ STR
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Preset []. This option applies multiple options at the same time. It should be
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applied before other options because options applied later will overwrite the
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values set by
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.BR -x .
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Available
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.I STR
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are:
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.RS
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.TP 8
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.B ava-pb
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PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
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.TP 8
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
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.TP
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.B map10k
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PacBio/Oxford Nanopore read to reference mapping (-Hk19)
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.TP
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.B asm5
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Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200).
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Typically, the alignment will not extend to regions with 5% or higher sequence
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divergence. Only use this preset if the average divergence is far below 5%.
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.TP
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.B asm10
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Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up
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to 10% sequence divergence.
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.RE
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.TP
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.BI --max-chain-skip \ INT
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A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
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for chaining. The time complexity is quadratic in the number of seeds. This
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@ -265,6 +236,51 @@ use
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.TP
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.B -V
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Print version number to stdout
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.SS Preset options
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.TP 10
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.BI -x \ STR
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Preset []. This option applies multiple options at the same time. It should be
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applied before other options because options applied later will overwrite the
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values set by
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.BR -x .
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Available
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.I STR
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are:
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.RS
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.TP 8
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.B map-pb
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PacBio/Oxford Nanopore read to reference mapping (-Hk19)
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.TP
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.B map10k
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The same as
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.B map-pb
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(-Hk19)
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.TP
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.B map-ont
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Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For
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PacBio reads, HPC minimizers consistently leads to faster performance and more
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sensitive results in comparison to normal minimizers. For Oxford Nanopore data,
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normal minimizers are better, though not much. The effectiveness of HPC is
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determined by the sequencing error mode.
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.TP
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.B asm5
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Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200).
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Typically, the alignment will not extend to regions with 5% or higher sequence
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divergence. Only use this preset if the average divergence is far below 5%.
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.TP
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.B asm10
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Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up
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to 10% sequence divergence.
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.TP 8
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.B ava-pb
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PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25)
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.TP 8
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000
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--max-chain-skip 25). Similarly, the major difference from
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.B ava-pb
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is that this preset is not using HPC minimizers.
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.RE
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.SS Miscellaneous options
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.TP 10
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.B --no-kalloc
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