From f41bb0e327214cb30de2f247ed53c6851872b836 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 24 Nov 2017 10:59:58 -0500 Subject: [PATCH] manpage --- minimap2.html | 643 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 643 insertions(+) create mode 100644 minimap2.html diff --git a/minimap2.html b/minimap2.html new file mode 100644 index 0000000..042446e --- /dev/null +++ b/minimap2.html @@ -0,0 +1,643 @@ + + +Manual Page - minimap2(1) + +
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+

Manual Reference Pages  - minimap2 (1)

+
+ + +

NAME

+ + +
+

+minimap2 - mapping and alignment between collections of DNA sequences +

+

CONTENTS

+
+Synopsis
+Description
+Options
+     Indexing options
+     Mapping options
+     Alignment options
+     Input/output options
+     Preset options
+     Miscellaneous options
+Output Format
+Limitations
+See Also
+
+ + +

SYNOPSIS

+ + +
+* Indexing the target sequences (optional): +
+minimap2 +[-x preset] -d target.mmi target.fa
+minimap2 +[-H] [-k kmer] [-w miniWinSize] [-I batchSize] -d target.mmi target.fa
+

+* Long-read alignment with CIGAR: +

+minimap2 +-a [-x preset] target.mmi query.fa > +output.sam
+minimap2 +-c [-H] [-k kmer] [-w miniWinSize] [...] target.fa query.fa > +output.paf
+

+* Long-read overlap without CIGAR: +

+minimap2 +-x ava-ont +[-t nThreads] target.fa query.fa > +output.paf
+
+ + +

DESCRIPTION

+ + +
+

+Minimap2 is a fast sequence mapping and alignment program that can find +overlaps between long noisy reads, or map long reads or their assemblies to a +reference genome optionally with detailed alignment (i.e. CIGAR). At present, +it works efficiently with query sequences from a few kilobases to ~100 +megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the +SAM format. +

+ + +

OPTIONS

+ + +
+
+ + +

    Indexing options

+ +
+ + + + + + +
+-k INT +Minimizer k-mer length [15] +
+-w INT +Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer +in a window of w consecutive k-mers. +
+-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 +on the HPC sequence. +
+-I NUM +Load at most +NUM target bases into RAM for indexing [4G]. 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. +NUM may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a +multi-part index. +
+-d FILE +Save the minimizer index of +target.fa to +FILE [no dump]. Minimap2 indexing is fast. It can index the human genome in a couple +of minutes. If even shorter startup time is desired, use this option to save +the index. Indexing options are fixed in the index file. When an index file is +provided as the target sequences, options +-H, -k, -w, -I will be effectively overridden by the options stored in the index file. +
+ + +

    Mapping options

+ +
+ + + + + + + + + + + + + + + + +
+-f FLOAT +Ignore top +FLOAT fraction of most frequent minimizers [0.0002] +
+-g INT +Stop chain enlongation if there are no minimizers in +INT-bp [10000]. +
+-r INT +Bandwidth used in chaining and DP-based alignment [500]. This option +approximately controls the maximum gap size. +
+-n INT +Discard chains consisting of +<INT number of minimizers [3] +
+-m INT +Discard chains with chaining score +<INT [40]. Chaining score equals the approximate number of matching bases minus a +concave gap penalty. It is computed with dynamic programming. +
+-X +Perform all-vs-all mapping. In this mode, if the query sequence name is +lexicographically larger than the target sequence name, the hits between them +will be suppressed; if the query sequence name is the same as the target name, +diagonal minimizer hits will also be suppressed. +
+-p FLOAT +Minimal secondary-to-primary score ratio to output secondary mappings [0.8]. +Between two chains overlaping over half of the shorter chain (controlled by +--mask-level), the chain with a lower score is secondary to the chain with a higher score. +If the ratio of the scores is below +FLOAT, the secondary chain will not be outputted or extended with DP alignment later. +
+-N INT +Output at most +INT secondary alignments [5]. This option has no effect when +-X is applied. +
+-G NUM +Maximum gap on the reference (effective with +-xsplice/--splice). This option also changes the chaining and alignment band width to +NUM. Increasing this option slows down spliced alignment. [200k] +
+-F NUM +Maximum fragment length (aka insert size; effective with +-xsr/--frag) [800] +
+--max-chain-skip INT
  +A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming +for chaining. The time complexity is quadratic in the number of seeds. This +option makes minimap2 exits the inner loop if it repeatedly sees seeds already +on chains. Set +INT to a large number to switch off this heurstics. +
+--no-long-join
  +Disable the long gap patching heuristic. When this option is applied, the +maximum alignment gap is mostly controlled by +-r.
+--splice +Enable the splice alignment mode. +
+--sr +Enable short-read alignment heuristics. In the short-read mode, minimap2 +applies a second round of chaining with a higher minimizer occurrence threshold +if no good chain is found. In addition, minimap2 attempts to patch gaps between +seeds with ungapped alignment. +
+--frag[=no|yes]
  +Whether to enable the fragment mode [no] +
+ + +

    Alignment options

+ +
+ + + + + + + + + + + +
+-A INT +Matching score [2] +
+-B INT +Mismatching penalty [4] +
+-O INT1[,INT2]
  +Gap open penalty [4,24]. If +INT2 is not specified, it is set to +INT1.
+-E INT1[,INT2]
  +Gap extension penalty [2,1]. A gap of length +k costs +min{O1+k*E1,O2+k*E2}. In the splice mode, the second gap penalties are not used. +
+-C INT +Cost for a non-canonical GT-AG splicing (effective with +--splice) [0] +
+-z INT +Break an alignment if the running score drops too quickly along the diagonal of +the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves +the contiguity of the alignment at the cost of poor alignment in the middle +(e.g. caused by a long inversion). +
+-s INT +Minimal peak DP alignment score to output [40]. The peak score is computed from +the final CIGAR. It is the score of the max scoring segment in the alignment +and may be different from the total alignment score. +
+-u CHAR +How to find canonical splicing sites GT-AG - +f: transcript strand; +b: both strands; +n: no attempt to match GT-AG [n] +
+--end-bonus INT
  +Score bonus when alignment extends to the end of the query sequence [0]. +
+--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 +base to a +AG acceptor tends to be C/T [yes with +--splice]. This trend is evolutionarily conservative, all the way to S. cerevisiae +(PMID:18688272). Specifying this option generally leads to higher junction +accuracy by several percents, so it is applied by default with +--splice. However, the SIRV control does not honor this trend +(only ~60%). This option reduces accuracy. If you are benchmarking minimap2 +on SIRV data, please add +--splice-flank=no to the command line. +
+ + +

    Input/output options

+ +
+ + + + + + + + + + + + + + +
+-a +Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF +by default. +
+-Q +Ignore base quality in the input file. +
+-L +Write CIGAR with >65535 operators at the CG tag. Older tools are unable to +convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM +compatible with older tools. Newer tools recognizes this tag and reconstruct +the real CIGAR in memory. +
+-R STR +SAM read group line in a format like +@RG\\tID:foo\\tSM:bar []. +
+-c +Generate CIGAR. In PAF, the CIGAR is written to the ‘cg’ custom tag. +
+--cs[=STR]
  +Output the +cs tag. +STR can be either +short or +long. If no +STR is given, +short is assumed. [none] +
+-Y +In SAM output, use soft clipping for supplementary alignments. +
+--seed INT +Integer seed for randomizing equally best hits. Minimap2 hashes +INT and read name when choosing between equally best hits. [11] +
+-t INT +Number of threads [3]. Minimap2 uses at most three threads when indexing target +sequences, and uses up to +INT+1 threads when mapping (the extra thread is for I/O, which is frequently idle and +takes little CPU time). +
+-2 +Use two I/O threads during mapping. By default, minimap2 uses one I/O thread. +When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O +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. +
+-K NUM +Number of bases loaded into memory to process in a mini-batch [500M]. +Similar to option +-I, K/M/G/k/m/g suffix is accepted. A large +NUM helps load balancing in the multi-threading mode, at the cost of increased +memory. +
+--secondary[=yes|no]
  +Whether to output secondary alignments [yes] +
+--version +Print version number to stdout +
+ + +

    Preset options

+ +
+ + +
+-x STR +Preset []. This option applies multiple options at the same time. It should be +applied before other options because options applied later will overwrite the +values set by +-x. Available +STR are: + + + + + + + + + + +
+map-pb +PacBio/Oxford Nanopore read to reference mapping +(-Hk19)
+map-ont +Slightly more sensitive for Oxford Nanopore to reference mapping +(-k15). For PacBio reads, HPC minimizers consistently leads to faster performance and +more sensitive results in comparison to normal minimizers. For Oxford Nanopore +data, normal minimizers are better, though not much. The effectiveness of HPC +is determined by the sequencing error mode. +
+asm5 +Long assembly to reference mapping +(-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200). 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%. +
+asm10 +Long assembly to reference mapping +(-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up to 10% sequence divergence. +
+ava-pb +PacBio all-vs-all overlap mapping +(-Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25).
+ava-ont +Oxford Nanopore all-vs-all overlap mapping +(-k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25). Similarly, the major difference from +ava-pb is that this preset is not using HPC minimizers. +
+splice +Long-read spliced alignment +(-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --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 +‘ms’ tag ignores introns to demote hits to pseudogenes. +
+sr +Short single-end reads without splicing +(-k21 -w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --secondary=no).
+ + +

    Miscellaneous options

+ +
+ + + + +
+--no-kalloc
  +Use the libc default allocator instead of the kalloc thread-local allocator. +This debugging option is mostly used with Valgrind to detect invalid memory +accesses. Minimap2 runs slower with this option, especially in the +multi-threading mode. +
+--print-qname
  +Print query names to stderr, mostly to see which query is crashing minimap2. +
+--print-seeds
  +Print seed positions to stderr, for debugging only. +
+ + +

OUTPUT FORMAT

+ + +
+

+Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by +default. PAF is a TAB-delimited text format with each line consisting of at +least 12 fields as are described in the following table: +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
ColTypeDescription
1stringQuery sequence name
2intQuery sequence length
3intQuery start coordinate (0-based)
4intQuery end coordinate (0-based)
5char‘+’ if query/target on the same strand; ‘-’ if opposite
6stringTarget sequence name
7intTarget sequence length
8intTarget start coordinate on the original strand
9intTarget end coordinate on the original strand
10intNumber of matching bases in the mapping
11intNumber bases, including gaps, in the mapping
12intMapping quality (0-255 with 255 for missing)
+

+

+When alignment is available, column 11 gives the total number of sequence +matches, mismatches and gaps in the alignment; column 10 divided by column 11 +gives the BLAST-like alignment identity. When alignment is unavailable, +these two columns are approximate. PAF may optionally have additional fields in +the SAM-like typed key-value format. Minimap2 may output the following tags: +

+ + + + + + + + + + + + + + + + + + + + + + + + + +
TagTypeDescription
tpAType of aln: P/primary, S/secondary and I/inversion
cmiNumber of minimizers on the chain
s1iChaining score
s2iChaining score of the best secondary chain
NMiTotal number of mismatches and gaps in the alignment
ASiDP alignment score
msiDP score of the max scoring segment in the alignment
nniNumber of ambiguous bases in the alignment
tsATranscript strand (splice mode only)
cgZCIGAR string (only in PAF)
csZDifference string
+

+

+The +cs tag encodes difference sequences in the short form or the entire query +AND reference sequences in the long form. It consists of a series of operations: +

+ + + + + + + + + + + + + + + +
OpRegexDescription
=[ACGTN]+Identical sequence (long form)
:[0-9]+Identical sequence length
*[acgtn][acgtn]Substitution: ref to query
+[acgtn]+Insertion to the reference
-[acgtn]+Deletion from the reference
~[acgtn]{2}[0-9]+[acgtn]{2}Intron length and splice signal
+

+

+ + +

LIMITATIONS

+ + +
+ + + +
+* + +Minimap2 may produce suboptimal alignments through long low-complexity regions +where seed positions may be suboptimal. This should not be a big concern +because even the optimal alignment may be wrong in such regions. +
+* + +Minimap2 requires SSE2 instructions to compile. It is possible to add +non-SSE2 support, but it would make minimap2 slower by several times. +
+ + +

SEE ALSO

+ + +
+

+miniasm(1), minimap(1), bwa(1). +

+

+
minimap2-2.5 (r572) minimap2 (1) 11 November 2017