r1034: changed multiple defaults; updated manpage
This commit is contained in:
Heng Li
parent
bbb4f97e52
commit
6c96078ed0
5
main.c
5
main.c
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@ -7,7 +7,7 @@
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#include "mmpriv.h"
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#include "ketopt.h"
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#define MM_VERSION "2.18-r1028-dirty"
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#define MM_VERSION "2.18-r1034-dirty"
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#ifdef __linux__
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#include <sys/resource.h>
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@ -339,7 +339,8 @@ int main(int argc, char *argv[])
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fprintf(fp_help, " --version show version number\n");
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fprintf(fp_help, " Preset:\n");
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fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
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fprintf(fp_help, " - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
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fprintf(fp_help, " - map-pb/map-ont - PacBio CLR/Nanopore vs reference mapping\n");
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fprintf(fp_help, " - map-hifi - PacBio HiFi reads vs reference mapping\n");
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fprintf(fp_help, " - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
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fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
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fprintf(fp_help, " - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
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98
minimap2.1
98
minimap2.1
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@ -145,18 +145,25 @@ or
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.B -xsr
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mode, which sets the threshold for a second round of seeding.
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.TP
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.BI --min-occ-floor \ INT
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Force minimap2 to always use k-mers occurring
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.I INT
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times or less [0]. In effect, the max occurrence threshold is set to
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the
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.RI max{ INT ,
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.BR -f }.
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.BI -U \ INT1 [, INT2 ]
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Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
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.RI max{ INT1 ,\ min{ INT2 ,
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.BR -f }}.
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This option prevents excessively small or large
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.B -f
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estimated from the input reference. It deprecates
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.B --min-occ-floor
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in earlier versions of minimap2.
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.TP
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.BI -g \ INT
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.BI -e \ INT
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Sample a high-frequency minimizer every
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.I INT
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basepairs [500].
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.TP
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.BI -g \ NUM
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Stop chain enlongation if there are no minimizers within
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.IR INT -bp
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[10000].
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.IR NUM -bp
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[10k].
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.TP
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.BI -r \ INT
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Bandwidth used in chaining and DP-based alignment [500]. This option
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@ -234,6 +241,10 @@ Mark as secondary a chain that overlaps with a better chain by
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.I FLOAT
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or more of the shorter chain [0.5]
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.TP
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.BR --rmq = no | yes
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Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
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for aligning contigs through long INDELs.
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.TP
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.B --hard-mask-level
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Honor option
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.B -M
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@ -412,7 +423,7 @@ alignment.
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.BI --cap-sw-mem \ NUM
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Skip alignment if the DP matrix size is above
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.IR NUM .
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Set 0 to disable [0].
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Set 0 to disable [100m].
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.SS Input/output options
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.TP 10
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.B -a
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@ -523,66 +534,47 @@ Available
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.I STR
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are:
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.RS
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.TP 9
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.B map-pb
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PacBio/Oxford Nanopore read to reference mapping
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.RB ( -Hk19 )
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.TP
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.TP 10
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.B map-ont
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Slightly more sensitive for Oxford Nanopore to reference mapping
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.RB ( -k15 ).
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For PacBio reads, HPC minimizers consistently leads to faster performance and
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more sensitive results in comparison to normal minimizers. For Oxford Nanopore
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data, normal minimizers are better, though not much. The effectiveness of HPC
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is determined by the sequencing error mode.
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Align noisy long reads of ~10% error rate to a reference genome. This is the
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default mode.
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.TP
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.B map-hifi
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PacBio HiFi reads to reference mapping
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Align PacBio high-fidelity (HiFi) reads to a reference genome
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.RB ( -k19
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.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k
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.BR -U100,500 ).
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.B -w19 -U50,500 -A1 -B4 -O6,26 -E2,1
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.BR -s200 ).
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.TP
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.B map-pb
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Align older PacBio continuous long (CLR) reads to a reference genome
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.RB ( -Hk19 ).
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.TP
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.B asm5
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Long assembly to reference mapping
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.RB ( -k19
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.B -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50
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.BR --min-occ-floor=100 ).
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.B -w19 -U50,500 --rmq -r100k --no-long-join -A1 -B19 -O39,81 -E3,1 -s200 -z200
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.BR -N50 ).
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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
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.RB ( -k19
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.B -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50
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.BR --min-occ-floor=100 ).
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.B -w19 -U50,500 --rmq -r100k --no-long-join -A1 -B9 -O16,41 -E2,1 -s200 -z200
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.BR -N50 ).
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Up to 10% sequence divergence.
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.TP
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.B asm20
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Long assembly to reference mapping
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.RB ( -k19
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.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50
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.BR --min-occ-floor=100 ).
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.B -w10 -U50,500 --rmq -r100k --no-long-join -A1 -B4 -O6,26 -E2,1 -s200 -z200
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.BR -N50 ).
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Up to 20% sequence divergence.
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.TP
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.B ava-pb
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PacBio all-vs-all overlap mapping
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.RB ( -Hk19
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.B -Xw5 -m100 -g10000 --max-chain-skip
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.BR 25 ).
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.TP
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping
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.RB ( -k15
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.B -Xw5 -m100 -g10000 -r2000 --max-chain-skip
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.BR 25 ).
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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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.TP
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.B splice
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Long-read spliced alignment
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.RB ( -k15
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.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9
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.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
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.BR --splice-flank=yes ).
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In the splice mode, 1) long deletions are taken as introns and represented as
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the
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@ -604,6 +596,18 @@ Short single-end reads without splicing
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.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
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.B -s40 -g200 -2K50m --heap-sort=yes
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.BR --secondary=no ).
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.TP
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.B ava-pb
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PacBio CLR all-vs-all overlap mapping
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.RB ( -Hk19
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.B -Xw5 -e0
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.BR -m100 ).
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.TP
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.B ava-ont
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Oxford Nanopore all-vs-all overlap mapping
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.RB ( -k15
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.B -Xw5 -e0 -m100
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.BR -r2k ).
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.RE
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.SS Miscellaneous options
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.TP 10
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25
options.c
25
options.c
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@ -16,7 +16,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
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memset(opt, 0, sizeof(mm_mapopt_t));
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opt->seed = 11;
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opt->mid_occ_frac = 2e-4f;
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opt->max_mid_occ = 1000000000;
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opt->min_mid_occ = 10;
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opt->max_mid_occ = 1000000;
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opt->sdust_thres = 0; // no SDUST masking
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opt->min_cnt = 3;
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@ -63,12 +64,13 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
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{
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if ((opt->flag & MM_F_SPLICE_FOR) || (opt->flag & MM_F_SPLICE_REV))
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opt->flag |= MM_F_SPLICE;
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if (opt->mid_occ <= 0)
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if (opt->mid_occ <= 0) {
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opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
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if (opt->mid_occ < opt->min_mid_occ)
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opt->mid_occ = opt->min_mid_occ;
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if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
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opt->mid_occ = opt->max_mid_occ;
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if (opt->mid_occ < opt->min_mid_occ)
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opt->mid_occ = opt->min_mid_occ;
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if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
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opt->mid_occ = opt->max_mid_occ;
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}
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if (mm_verbose >= 3)
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fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
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}
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@ -88,26 +90,27 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
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} else if (strcmp(preset, "ava-ont") == 0) {
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io->flag = 0, io->k = 15, io->w = 5;
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mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
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mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
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mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_chain_skip = 25;
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mo->bw = 2000;
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mo->occ_dist = 0;
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} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
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io->flag |= MM_I_HPC, io->k = 19;
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} else if (strcmp(preset, "ava-pb") == 0) {
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io->flag |= MM_I_HPC, io->k = 19, io->w = 5;
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mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
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mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
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mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_chain_skip = 25;
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mo->occ_dist = 0;
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} else if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
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io->flag = 0, io->k = 19, io->w = 19;
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mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
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mo->max_gap = 10000;
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mo->occ_dist = 500;
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mo->min_mid_occ = 100, mo->max_mid_occ = 500;
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mo->min_mid_occ = 50, mo->max_mid_occ = 500;
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mo->min_dp_max = 200;
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} else if (strncmp(preset, "asm", 3) == 0) {
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io->flag = 0, io->k = 19, io->w = 19;
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mo->bw = 100000;
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mo->flag |= MM_F_RMQ | MM_F_NO_LJOIN;
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mo->min_mid_occ = 100, mo->max_mid_occ = 500;
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mo->min_mid_occ = 50, mo->max_mid_occ = 500;
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mo->min_dp_max = 200;
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mo->best_n = 50;
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if (strcmp(preset, "asm5") == 0) {
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