145 lines
2.7 KiB
Groff
145 lines
2.7 KiB
Groff
.TH minimap2 1 "30 June 2017" "minimap2-2.0-r126-pre" "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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.SH SYNOPSIS
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* Indexing the target sequences (optional):
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.RS 4
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minimap2
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.RB [ -H ]
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.RB [ -k
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.IR kmer ]
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.RB [ -w
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.IR miniWinSize ]
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.RB [ -I
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.IR batchSize ]
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.B -d
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.I target.mmi
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.I target.fa
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.RE
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* Long-read alignment with CIGAR:
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.RS 4
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minimap2
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.B -b
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.RB [ -x
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.IR preset ]
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.I target.mmi
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.I query.fa
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>
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.I output.sam
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.br
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minimap2
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.B -c
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.RB [ -H ]
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.RB [ -k
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.IR kmer ]
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.RB [ -w
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.IR miniWinSize ]
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.RB [ ... ]
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.I target.fa
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.I query.fa
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>
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.I output.paf
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.RE
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* Long-read overlap without CIGAR:
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.RS 4
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minimap2
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.B -x
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ava10k
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.RB [ -t
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.IR nThreads ]
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.I target.fa
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.I query.fa
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>
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.I output.paf
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.RE
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.SH DESCRIPTION
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.PP
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Minimap2 is a fast sequence mapping and alignment program that can find
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overlaps between long noisy reads, or map long reads or their assemblies to a
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reference genome optionally with detailed alignment (i.e. CIGAR). At present,
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it works efficiently with query sequences from a few kilobases to ~100
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megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
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SAM format.
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.SH OPTIONS
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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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.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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in a window of w consecutive k-mers.
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.TP
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.B -H
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Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
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contracting homopolymer runs to a single base. An HPC minimizer is a minimizer
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on the HPC sequence.
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.TP
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.BI -I \ NUM
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Load at most
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.I NUM
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target bases into RAM for indexing [4G]. If there are more than
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.I NUM
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bases in
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.IR target.fa ,
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minimap2 needs to read
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.I query.fa
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multiple times to map it against each batch of target sequences.
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.I NUM
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may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
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multi-part index.
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.TP
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.BI -d \ FILE
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Save the minimizer index of
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.I target.fa
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to
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.I FILE
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[no dump]
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.SS Mapping options
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.TP 10
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.BI -f \ FLOAT
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Ignore top
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.I FLOAT
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fraction of most frequent minimizers [0.0002]
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.SH OUTPUT FORMAT
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.TS
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center box;
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cb | cb | cb
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r | c | l .
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Col Type Description
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_
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1 string Query sequence name
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2 int Query sequence length
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3 int Query start coordinate (0-based)
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4 int Query end coordinate (0-based)
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5 char `+' if query and target on the same strand; `-' if opposite
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6 string Target sequence name
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7 int Target sequence length
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8 int Target start coordinate on the original strand
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9 int Target end coordinate on the original strand
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10 int Number of matching bases in the mapping
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11 int Number bases, including gaps, in the mapping
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12 int Mapping quality (0-255 with 255 for missing)
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.TE
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.SH SEE ALSO
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.PP
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miniasm(1), minimap(1), bwa(1).
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