53 lines
946 B
Groff
53 lines
946 B
Groff
.TH minimap 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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* Index 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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.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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* Align 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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.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). For
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reference-based alignment, it works efficiently with query sequences from a few
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kilobases to ~100 megabases in length at a error rate ~15%.
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