diff --git a/minimap2.html b/minimap2.html index b371583..f394ac6 100644 --- a/minimap2.html +++ b/minimap2.html @@ -61,7 +61,7 @@ p { text-align: justify; } -Manual Page - minimap2(1) +minimap2.1
@@ -153,10 +153,19 @@ Minimizer k-mer length [15] -w INT -Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer +Minimizer window size [10]. A minimizer is the smallest k-mer in a window of w consecutive k-mers. +-j INT +Syncmer submer size [10]. Option +-j and +-w will override each: if +-w is applied after +-j, -j will have no effect, and vice versa. +

+ + -H Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by contracting homopolymer runs to a single base. An HPC minimizer is a minimizer @@ -165,13 +174,13 @@ on the HPC sequence. -I NUM Load at most -NUM target bases into RAM for indexing [4G]. If there are more than +NUM target bases into RAM for indexing [8G]. If there are more than NUM bases in target.fa, minimap2 needs to read -query.fa multiple times to map it against each batch of target sequences. +query.fa multiple times to map it against each batch of target sequences. This would create a multi-part index. NUM may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a -multi-part index. - +multi-part index. See also option +--split-prefix. --idx-no-seq   Don’t store target sequences in the index. It saves disk space and memory but @@ -316,6 +325,11 @@ Use the minigraph chaining algorithm [no]. The minigraph algorithm is better for aligning contigs through long INDELs. +--rmq-inner NUM   +Apply full dynamic programming for anchors within distance +NUM [1000]. + + --hard-mask-level   Honor option -M and disable a heurstic to save unmapped subsequences and disables @@ -387,6 +401,10 @@ faster for short reads, but slower for long reads. [no] Treat two reads in a pair as independent reads. The mate related fields in SAM are still properly populated. + +--no-hash-name   +Produce the same alignment for identical sequences regardless of their sequence names. + @@ -402,6 +420,10 @@ Matching score [2] -B INT Mismatching penalty [4] + +-b INT +Mismatching penalty for transitions [same as +-B]. -O INT1[,INT2]   Gap open penalty [4,24]. If @@ -414,9 +436,15 @@ Gap extension penalty [2,1]. A gap of length min{O1+k*E1,O2+k*E2}. In the splice mode, the second gap penalties are not used. +-J INT +Splice model [1]. 0 for the original minimap2 splice model that always penalizes non-GT-AG splicing; +1 for the miniprot model that considers non-GT-AG. Option +-C has no effect with the default +-J1. -J0. + -C INT Cost for a non-canonical GT-AG splicing (effective with ---splice) [0] +--splice -J0) [0]. -z INT1[,INT2]   @@ -454,6 +482,11 @@ Score bonus when alignment extends to the end of the query sequence [0]. Score of a mismatch involving ambiguous bases [1]. +--pe-ind-chain   +For paired-end short reads, perform chaining for each end independently. +By default, minimap2 chains the two ends together. + + --splice-flank=yes|no   Assume the next base to a GT donor site tends to be A/G (91% in human and 92% in mouse) and the preceding @@ -467,6 +500,20 @@ accuracy by several percents, so it is applied by default with on SIRV data, please add --splice-flank=no to the command line. + +--spsc FILE +Splice scores []. Each line consists of five fields: 1) contig, 2) offset, 3) ‘+’ or ‘-’, 4) ‘D’ or ‘A’, and 5) score, +where offset is the number of bases before a splice junction, ‘D’ indicates the +line corresponds to a donor site and ‘A’ for an acceptor site. +A positive score suggests the junction is preferred and a negative score +suggests the junction is not preferred. + + +--junc-pen INT   +Penalty for a position not in FILE specified by +--spsc [5]. Effective with +--spsc but not +--junc-bed. --junc-bed FILE   Gene annotations in the BED12 format (aka 12-column BED), or intron positions @@ -476,9 +523,9 @@ BED12 file can be converted from GTF/GFF3 with ‘paftools.js gff2bed anno.gt --junc-bonus INT   -Score bonus for a splice donor or acceptor found in annotation (effective with ---junc-bed) [9]. - +Score bonus for a splice donor or acceptor found in annotation [9]. Effective with +--junc-bed but not +--spsc. --end-seed-pen INT   Drop a terminal anchor if @@ -501,7 +548,7 @@ Skip alignment if the DP matrix size is above --cap-kalloc NUM   Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above -NUM. Set 0 to disable [0]. +NUM. Set 0 to disable [500m]. @@ -566,6 +613,10 @@ Output =/X CIGAR operators for sequence match/mismatch. -Y In SAM output, use soft clipping for supplementary alignments. + +--secondary-seq   +In SAM output, show query sequences for secondary alignments. + --seed INT Integer seed for randomizing equally best hits. Minimap2 hashes @@ -638,33 +689,52 @@ Align noisy long reads of ~10% error rate to a reference genome. This is the default mode. +lr:hq +Align accurate long reads (error rate <1%) to a reference genome +(-k19 -w19 -U50,500 -g10k). This was recommended by ONT developers for recent Nanopore reads +produced with chemistry v14 that can reach ~99% in accuracy. +It was shown to work better for accurate Nanopore reads +than +map-hifi. + map-hifi Align PacBio high-fidelity (HiFi) reads to a reference genome -(-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200). +(-xlr:hq -A1 -B4 -O6,26 -E2,1 -s200). It differs from +lr:hq only in scoring. It has not been tested whether +lr:hq would work better for PacBio HiFi reads. + map-pb Align older PacBio continuous long (CLR) reads to a reference genome -(-Hk19). +(-Hk19). Note that this data type is effectively deprecated by HiFi. +Unless you work on very old data, you probably want to use +map-hifi or +lr:hq. + +map-iclr +Align Illumina Complete Long Reads (ICLR) to a reference genome +(-k19 -B6 -b4 -O10,50). This was recommended by Illumina developers. + asm5 Long assembly to reference mapping -(-k19 -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50). Typically, the alignment will not extend to regions with 5% or higher sequence -divergence. Only use this preset if the average divergence is far below 5%. +(-k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50). Typically, the alignment will not extend to regions with 5% or higher sequence +divergence. Use this preset if the average divergence is not much higher than 0.1%. asm10 Long assembly to reference mapping -(-k19 -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50). Up to 10% sequence divergence. +(-k19 -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50). Use this if the average divergence is around 1%. asm20 Long assembly to reference mapping -(-k19 -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50). Up to 20% sequence divergence. +(-k19 -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50). Use this if the average divergence is around several percent. splice Long-read spliced alignment -(-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as +(-k15 -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0 --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the ‘N’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap costs are different during chaining; 4) the computation of the @@ -672,12 +742,16 @@ costs are different during chaining; 4) the computation of the splice:hq -Long-read splice alignment for PacBio CCS reads +Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq (-xsplice -C5 -O6,24 -B4). +splice:sr +Spliced alignment for short RNA-seq reads +(-xsplice:hq --frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain --secondary=no). + sr -Short single-end reads without splicing -(-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g100 -2K50m --heap-sort=yes --secondary=no). +Short-read alignment without splicing +(-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m25 -s40 -g100 -2K50m --heap-sort=yes --secondary=no). ava-pb PacBio CLR all-vs-all overlap mapping @@ -775,7 +849,7 @@ the SAM-like typed key-value format. Minimap2 may output the following tags: ASiDP alignment score -SAZList of other supplementary alignments +SAZList of other supplementary alignments (with approximate CIGAR strings) msiDP score of the max scoring segment in the alignment @@ -848,4 +922,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times. miniasm(1), minimap(1), bwa(1).

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minimap2-2.23 (r1111) minimap2 (1) 18 November 2021
+
minimap2-2.28-dirty (r1237) minimap2 (1) 30 March 2025