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<TITLE>Manual Page - minimap2(1)</TITLE>
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<BODY bgcolor=#F0F0F0 text=#000000 link=#0000ff vlink=#C000C0 alink=#ff0000><div id="wrap"><A NAME=top></A>
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<CENTER>
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<H1><HR><I>Manual Reference Pages - </I><NOBR>minimap2 (1)</NOBR><HR></H1>
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</CENTER>
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<A name=0></A>
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<H3>NAME</H3>
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<BLOCKQUOTE>
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<P>
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minimap2 - mapping and alignment between collections of DNA sequences
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</BLOCKQUOTE>
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<A name=contents></A><H3>CONTENTS</H3></A>
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<BLOCKQUOTE>
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<A HREF=#1>Synopsis</A><BR>
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<A HREF=#2>Description</A><BR>
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<A HREF=#3>Options</A><BR>
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<A HREF=#4>Indexing options</A><BR>
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<A HREF=#5>Mapping options</A><BR>
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<A HREF=#6>Alignment options</A><BR>
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<A HREF=#7>Input/output options</A><BR>
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<A HREF=#8>Preset options</A><BR>
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<A HREF=#9>Miscellaneous options</A><BR>
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<A HREF=#10>Output Format</A><BR>
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<A HREF=#11>Limitations</A><BR>
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<A HREF=#12>See Also</A><BR>
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</BLOCKQUOTE>
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<A name=13></A>
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<H3>SYNOPSIS</H3>
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<BLOCKQUOTE>
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* Indexing the target sequences (optional):
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<BLOCKQUOTE>
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minimap2
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[<B>-x</B> <I>preset</I>] <B>-d</B> <I>target.mmi</I> <I>target.fa</I> <!-- Need break --><BR>
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minimap2
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[<B>-H</B>] [<B>-k</B> <I>kmer</I>] [<B>-w</B> <I>miniWinSize</I>] [<B>-I</B> <I>batchSize</I>] <B>-d</B> <I>target.mmi</I> <I>target.fa</I> </BLOCKQUOTE>
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<P>
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* Long-read alignment with CIGAR:
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<BLOCKQUOTE>
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minimap2
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<B>-a</B> [<B>-x</B> <I>preset</I>] <I>target.mmi</I> <I>query.fa</I> >
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<I>output.sam</I> <!-- Need break --><BR>
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minimap2
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<B>-c</B> [<B>-H</B>] [<B>-k</B> <I>kmer</I>] [<B>-w</B> <I>miniWinSize</I>] [<B>...</B>] <I>target.fa</I> <I>query.fa</I> >
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<I>output.paf</I> </BLOCKQUOTE>
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<P>
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* Long-read overlap without CIGAR:
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<BLOCKQUOTE>
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minimap2
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<B>-x</B> ava-ont
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[<B>-t</B> <I>nThreads</I>] <I>target.fa</I> <I>query.fa</I> >
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<I>output.paf</I> </BLOCKQUOTE>
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</BLOCKQUOTE>
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<A name=2></A>
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<H3>DESCRIPTION</H3>
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<BLOCKQUOTE>
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<P>
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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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</BLOCKQUOTE>
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<A name=3></A>
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<H3>OPTIONS</H3>
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<BLOCKQUOTE>
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</BLOCKQUOTE>
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<A name=4></A>
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<H4> Indexing options</H4>
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<BLOCKQUOTE>
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<TABLE cellpadding=3>
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<TR valign=top><TD width=10% nowrap>
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<B>-k</B><I> INT</I> </TD><TD valign=bottom>
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Minimizer k-mer length [15]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-w</B><I> INT</I> </TD><TD valign=bottom>
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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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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-H</B> </TD><TD valign=bottom>
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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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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-I</B><I> NUM</I> </TD><TD valign=bottom>
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Load at most
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<I>NUM</I> target bases into RAM for indexing [4G]. If there are more than
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<I>NUM</I> bases in
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<I>target.fa</I>, minimap2 needs to read
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<I>query.fa</I> multiple times to map it against each batch of target sequences.
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<I>NUM</I> 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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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-d</B><I> FILE</I> </TD><TD valign=bottom>
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Save the minimizer index of
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<I>target.fa</I> to
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<I>FILE</I> [no dump]. Minimap2 indexing is fast. It can index the human genome in a couple
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of minutes. If even shorter startup time is desired, use this option to save
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the index. Indexing options are fixed in the index file. When an index file is
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provided as the target sequences, options
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<B>-H</B>, <B>-k</B>, <B>-w</B>, <B>-I</B> will be effectively overridden by the options stored in the index file.
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</TD></TR>
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<TR></TR></TABLE></BLOCKQUOTE>
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<A name=5></A>
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<H4> Mapping options</H4>
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<BLOCKQUOTE>
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<TABLE cellpadding=3>
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<TR valign=top><TD width=10% nowrap>
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<B>-f</B><I> FLOAT</I> </TD><TD valign=bottom>
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Ignore top
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<I>FLOAT</I> fraction of most frequent minimizers [0.0002]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-g</B><I> INT</I> </TD><TD valign=bottom>
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Stop chain enlongation if there are no minimizers in
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<I>INT</I>-bp [10000].
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-r</B><I> INT</I> </TD><TD valign=bottom>
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Bandwidth used in chaining and DP-based alignment [500]. This option
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approximately controls the maximum gap size.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-n</B><I> INT</I> </TD><TD valign=bottom>
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Discard chains consisting of
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<<I>INT</I> number of minimizers [3]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-m</B><I> INT</I> </TD><TD valign=bottom>
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Discard chains with chaining score
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<<I>INT</I> [40]. Chaining score equals the approximate number of matching bases minus a
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concave gap penalty. It is computed with dynamic programming.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-X</B> </TD><TD valign=bottom>
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Perform all-vs-all mapping. In this mode, if the query sequence name is
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lexicographically larger than the target sequence name, the hits between them
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will be suppressed; if the query sequence name is the same as the target name,
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diagonal minimizer hits will also be suppressed.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-p</B><I> FLOAT</I> </TD><TD valign=bottom>
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Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
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Between two chains overlaping over half of the shorter chain (controlled by
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<B>--mask-level</B>), the chain with a lower score is secondary to the chain with a higher score.
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If the ratio of the scores is below
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<I>FLOAT</I>, the secondary chain will not be outputted or extended with DP alignment later.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-N</B><I> INT</I> </TD><TD valign=bottom>
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Output at most
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<I>INT</I> secondary alignments [5]. This option has no effect when
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<B>-X</B> is applied.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-G</B><I> NUM</I> </TD><TD valign=bottom>
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Maximum gap on the reference (effective with
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<B>-xsplice</B>/<B>--splice</B>). This option also changes the chaining and alignment band width to
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<I>NUM</I>. Increasing this option slows down spliced alignment. [200k]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-F</B><I> NUM</I> </TD><TD valign=bottom>
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Maximum fragment length (aka insert size; effective with
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<B>-xsr</B>/<B>--frag)</B> [800]
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--max-chain-skip</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
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for chaining. The time complexity is quadratic in the number of seeds. This
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option makes minimap2 exits the inner loop if it repeatedly sees seeds already
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on chains. Set
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<I>INT</I> to a large number to switch off this heurstics.
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--no-long-join</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Disable the long gap patching heuristic. When this option is applied, the
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maximum alignment gap is mostly controlled by
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<B>-r</B>. </TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>--splice</B> </TD><TD valign=bottom>
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Enable the splice alignment mode.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>--sr</B> </TD><TD valign=bottom>
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Enable short-read alignment heuristics. In the short-read mode, minimap2
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applies a second round of chaining with a higher minimizer occurrence threshold
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if no good chain is found. In addition, minimap2 attempts to patch gaps between
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seeds with ungapped alignment.
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--frag</B>[=<B>no</B>|<B>yes</B>] </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Whether to enable the fragment mode [no]
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</TD></TR>
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<TR></TR></TABLE></BLOCKQUOTE>
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<A name=6></A>
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<H4> Alignment options</H4>
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<BLOCKQUOTE>
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<TABLE cellpadding=3>
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<TR valign=top><TD width=10% nowrap>
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<B>-A</B><I> INT</I> </TD><TD valign=bottom>
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Matching score [2]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-B</B><I> INT</I> </TD><TD valign=bottom>
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Mismatching penalty [4]
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>-O</B><I> INT1[,INT2]</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Gap open penalty [4,24]. If
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<I>INT2</I> is not specified, it is set to
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<I>INT1</I>. </TD></TR>
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<TR valign=top><TD colspan=2>
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<B>-E</B><I> INT1[,INT2]</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Gap extension penalty [2,1]. A gap of length
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<I>k</I> costs
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min{<I>O1</I>+<I>k</I>*<I>E1</I>,<I>O2</I>+<I>k</I>*<I>E2</I>}. In the splice mode, the second gap penalties are not used.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-C</B><I> INT</I> </TD><TD valign=bottom>
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Cost for a non-canonical GT-AG splicing (effective with
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<B>--splice</B>) [0]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-z</B><I> INT</I> </TD><TD valign=bottom>
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Break an alignment if the running score drops too quickly along the diagonal of
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the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves
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the contiguity of the alignment at the cost of poor alignment in the middle
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(e.g. caused by a long inversion).
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-s</B><I> INT</I> </TD><TD valign=bottom>
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Minimal peak DP alignment score to output [40]. The peak score is computed from
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the final CIGAR. It is the score of the max scoring segment in the alignment
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and may be different from the total alignment score.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-u</B><I> CHAR</I> </TD><TD valign=bottom>
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How to find canonical splicing sites GT-AG -
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<B>f</B>: transcript strand;
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<B>b</B>: both strands;
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<B>n</B>: no attempt to match GT-AG [n]
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--end-bonus</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Score bonus when alignment extends to the end of the query sequence [0].
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--splice-flank</B>[=<B>yes</B>|<B>no</B>] </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Assume the next base to a
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<B>GT</B> donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
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base to a
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<B>AG</B> acceptor tends to be C/T [yes with
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<B>--splice</B>]. This trend is evolutionarily conservative, all the way to S. cerevisiae
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(PMID:18688272). Specifying this option generally leads to higher junction
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accuracy by several percents, so it is applied by default with
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<B>--splice</B>. However, the SIRV control does not honor this trend
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(only ~60%). This option reduces accuracy. If you are benchmarking minimap2
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on SIRV data, please add
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<B>--splice-flank=no</B> to the command line.
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</TD></TR>
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<TR></TR></TABLE></BLOCKQUOTE>
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<A name=7></A>
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<H4> Input/output options</H4>
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<BLOCKQUOTE>
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<TABLE cellpadding=3>
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<TR valign=top><TD width=10% nowrap>
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<B>-a</B> </TD><TD valign=bottom>
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Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
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by default.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-Q</B> </TD><TD valign=bottom>
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Ignore base quality in the input file.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-L</B> </TD><TD valign=bottom>
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Write CIGAR with >65535 operators at the CG tag. Older tools are unable to
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convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM
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compatible with older tools. Newer tools recognizes this tag and reconstruct
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the real CIGAR in memory.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-R</B><I> STR</I> </TD><TD valign=bottom>
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SAM read group line in a format like
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<B>@RG\\tID:foo\\tSM:bar</B> [].
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-c</B> </TD><TD valign=bottom>
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Generate CIGAR. In PAF, the CIGAR is written to the ‘cg’ custom tag.
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</TD></TR>
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<TR valign=top><TD colspan=2>
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<B>--cs[=</B><I>STR</I><B>]</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
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Output the
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<B>cs</B> tag.
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<I>STR</I> can be either
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<I>short</I> or
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<I>long</I>. If no
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<I>STR</I> is given,
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<I>short</I> is assumed. [none]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-Y</B> </TD><TD valign=bottom>
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In SAM output, use soft clipping for supplementary alignments.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>--seed</B><I> INT</I> </TD><TD valign=bottom>
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Integer seed for randomizing equally best hits. Minimap2 hashes
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<I>INT</I> and read name when choosing between equally best hits. [11]
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-t</B><I> INT</I> </TD><TD valign=bottom>
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Number of threads [3]. Minimap2 uses at most three threads when indexing target
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sequences, and uses up to
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<I>INT</I>+1 threads when mapping (the extra thread is for I/O, which is frequently idle and
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takes little CPU time).
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
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<B>-2</B> </TD><TD valign=bottom>
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Use two I/O threads during mapping. By default, minimap2 uses one I/O thread.
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When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O
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thread may become the bottleneck. Apply this option to use one thread for input
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and another thread for output, at the cost of increased peak RAM.
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</TD></TR>
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<TR valign=top><TD width=10% nowrap>
|
|
<B>-K</B><I> NUM</I> </TD><TD valign=bottom>
|
|
Number of bases loaded into memory to process in a mini-batch [500M].
|
|
Similar to option
|
|
<B>-I</B>, K/M/G/k/m/g suffix is accepted. A large
|
|
<I>NUM</I> helps load balancing in the multi-threading mode, at the cost of increased
|
|
memory.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--secondary</B>[=<B>yes</B>|<B>no</B>] </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Whether to output secondary alignments [yes]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--version</B> </TD><TD valign=bottom>
|
|
Print version number to stdout
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=8></A>
|
|
|
|
<H4> Preset options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-x</B><I> STR</I> </TD><TD valign=bottom>
|
|
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
|
|
<B>-x</B>. Available
|
|
<I>STR</I> are:
|
|
<TABLE width=100% cellpadding=3><!-- tsb: Preset []. This option applies multiple options at the same time. It should be
|
|
-->
|
|
<TR></TR><TR></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>map-pb</B> </TD><TD valign=bottom>
|
|
PacBio/Oxford Nanopore read to reference mapping
|
|
(<B>-Hk19</B>) </TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>map-ont</B> </TD><TD valign=bottom>
|
|
Slightly more sensitive for Oxford Nanopore to reference mapping
|
|
(<B>-k15</B>). 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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>asm5</B> </TD><TD valign=bottom>
|
|
Long assembly to reference mapping
|
|
(<B>-k19</B> <B>-w19 -A1 -B19 -O39,81 -E3,1 -s200</B> <B>-z200</B>). 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%.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>asm10</B> </TD><TD valign=bottom>
|
|
Long assembly to reference mapping
|
|
(<B>-k19</B> <B>-w19 -A1 -B9 -O16,41 -E2,1 -s200</B> <B>-z200</B>). Up to 10% sequence divergence.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>ava-pb</B> </TD><TD valign=bottom>
|
|
PacBio all-vs-all overlap mapping
|
|
(<B>-Hk19</B> <B>-w5 -Xp0 -m100 -g10000 --max-chain-skip</B> <B>25</B>). </TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>ava-ont</B> </TD><TD valign=bottom>
|
|
Oxford Nanopore all-vs-all overlap mapping
|
|
(<B>-k15</B> <B>-w5 -Xp0 -m100 -g10000 --max-chain-skip</B> <B>25</B>). Similarly, the major difference from
|
|
<B>ava-pb</B> is that this preset is not using HPC minimizers.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>splice</B> </TD><TD valign=bottom>
|
|
Long-read spliced alignment
|
|
(<B>-k15</B> <B>-w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub</B> <B>--splice-flank=yes</B>). In the splice mode, 1) long deletions are taken as introns and represented as
|
|
the
|
|
‘<B>N</B>’ CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
|
|
costs are different during chaining; 4) the computation of the
|
|
‘<B>ms</B>’ tag ignores introns to demote hits to pseudogenes.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=8% nowrap>
|
|
<B>sr</B> </TD><TD valign=bottom>
|
|
Short single-end reads without splicing
|
|
(<B>-k21</B> <B>-w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20</B> <B>-s40 -g200 -2K50m</B> <B>--secondary=no</B>). </TD></TR>
|
|
<TR></TR></TABLE></TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=9></A>
|
|
|
|
<H4> Miscellaneous options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--no-kalloc</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--print-qname</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Print query names to stderr, mostly to see which query is crashing minimap2.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--print-seeds</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Print seed positions to stderr, for debugging only.
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=10></A>
|
|
|
|
<H3>OUTPUT FORMAT</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
<P>
|
|
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:
|
|
<P><BLOCKQUOTE><div id='tbl'><TABLE border=1 cellspacing=0 cellpadding=3>
|
|
<TR valign=top>
|
|
<TD align=center><B>Col</B></TD><TD align=center><B>Type</B></TD><TD align=center><B>Description</B></TD></TR>
|
|
<TR></TR><TR></TR>
|
|
<TR valign=top>
|
|
<TD align=right>1</TD><TD align=center>string</TD><TD>Query sequence name</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>2</TD><TD align=center>int</TD><TD>Query sequence length</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>3</TD><TD align=center>int</TD><TD>Query start coordinate (0-based)</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>4</TD><TD align=center>int</TD><TD>Query end coordinate (0-based)</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>5</TD><TD align=center>char</TD><TD>‘+’ if query/target on the same strand; ‘-’ if opposite</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>6</TD><TD align=center>string</TD><TD>Target sequence name</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>7</TD><TD align=center>int</TD><TD>Target sequence length</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>8</TD><TD align=center>int</TD><TD>Target start coordinate on the original strand</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>9</TD><TD align=center>int</TD><TD>Target end coordinate on the original strand</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>10</TD><TD align=center>int</TD><TD>Number of matching bases in the mapping</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>11</TD><TD align=center>int</TD><TD>Number bases, including gaps, in the mapping</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>12</TD><TD align=center>int</TD><TD>Mapping quality (0-255 with 255 for missing)</TD></TR>
|
|
</TABLE></div></BLOCKQUOTE>
|
|
<P>
|
|
<P>
|
|
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:
|
|
<P><BLOCKQUOTE><div id='tbl'><TABLE border=1 cellspacing=0 cellpadding=3>
|
|
<TR valign=top>
|
|
<TD align=center><B>Tag</B></TD><TD align=center><B>Type</B></TD><TD align=center><B>Description</B></TD></TR>
|
|
<TR></TR><TR></TR>
|
|
<TR valign=top>
|
|
<TD align=right>tp</TD><TD align=center>A</TD><TD>Type of aln: P/primary, S/secondary and I/inversion</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>cm</TD><TD align=center>i</TD><TD>Number of minimizers on the chain</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>s1</TD><TD align=center>i</TD><TD>Chaining score</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>s2</TD><TD align=center>i</TD><TD>Chaining score of the best secondary chain</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>NM</TD><TD align=center>i</TD><TD>Total number of mismatches and gaps in the alignment</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>AS</TD><TD align=center>i</TD><TD>DP alignment score</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>ms</TD><TD align=center>i</TD><TD>DP score of the max scoring segment in the alignment</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>nn</TD><TD align=center>i</TD><TD>Number of ambiguous bases in the alignment</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>ts</TD><TD align=center>A</TD><TD>Transcript strand (splice mode only)</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>cg</TD><TD align=center>Z</TD><TD>CIGAR string (only in PAF)</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>cs</TD><TD align=center>Z</TD><TD>Difference string</TD></TR>
|
|
</TABLE></div></BLOCKQUOTE>
|
|
<P>
|
|
<P>
|
|
The
|
|
<B>cs</B> tag encodes difference sequences in the short form or the entire query
|
|
<I>AND</I> reference sequences in the long form. It consists of a series of operations:
|
|
<P><BLOCKQUOTE><div id='tbl'><TABLE border=1 cellspacing=0 cellpadding=3>
|
|
<TR valign=top>
|
|
<TD align=center><B>Op</B></TD><TD align=center><B>Regex</B></TD><TD align=center><B>Description</B></TD></TR>
|
|
<TR></TR><TR></TR>
|
|
<TR valign=top>
|
|
<TD align=right> =</TD><TD>[ACGTN]+</TD><TD>Identical sequence (long form)</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right> :</TD><TD>[0-9]+</TD><TD>Identical sequence length</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right> *</TD><TD>[acgtn][acgtn]</TD><TD>Substitution: ref to query</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right> +</TD><TD>[acgtn]+</TD><TD>Insertion to the reference</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right> -</TD><TD>[acgtn]+</TD><TD>Deletion from the reference</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right> ~</TD><TD>[acgtn]{2}[0-9]+[acgtn]{2}</TD><TD>Intron length and splice signal</TD></TR>
|
|
</TABLE></div></BLOCKQUOTE>
|
|
<P>
|
|
</BLOCKQUOTE>
|
|
<A name=11></A>
|
|
|
|
<H3>LIMITATIONS</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD width=2% nowrap>
|
|
*
|
|
</TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=2% nowrap>
|
|
*
|
|
</TD><TD valign=bottom>
|
|
Minimap2 requires SSE2 instructions to compile. It is possible to add
|
|
non-SSE2 support, but it would make minimap2 slower by several times.
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=12></A>
|
|
|
|
<H3>SEE ALSO</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
<P>
|
|
miniasm(1), minimap(1), bwa(1).
|
|
</BLOCKQUOTE>
|
|
<P><HR>
|
|
<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.5 (r572)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>11 November 2017</I></TD> </TR></TABLE></div></BODY></HTML>
|