mirror of
https://github.com/lh3/minimap2.git
synced 2026-09-15 21:17:54 +08:00
852 lines
33 KiB
HTML
852 lines
33 KiB
HTML
<HTML><HEAD>
|
|
<style type="text/css">
|
|
a:link {
|
|
text-decoration: none;
|
|
color: #0092e8;
|
|
}
|
|
a:visited {
|
|
text-decoration: none;
|
|
color: #0092e8;
|
|
}
|
|
a:hover {
|
|
text-decoration: underline;
|
|
color: #0092e8;
|
|
}
|
|
body, td, th {
|
|
font: 12px consolas, andale mono, courier, mono;
|
|
}
|
|
body {
|
|
color: #000;
|
|
background: #fff;
|
|
margin: 0;
|
|
padding: 0;
|
|
}
|
|
table {
|
|
border: solid 0px #ccc;
|
|
}
|
|
td {
|
|
vertical-align: top;
|
|
padding: 0.2em;
|
|
}
|
|
th {
|
|
font-weight: bold;
|
|
text-align: left;
|
|
padding: 0.2em;
|
|
}
|
|
#tbl table {
|
|
border: solid 1px #ccc;
|
|
}
|
|
#tbl td {
|
|
border: solid 1px #ccc;
|
|
padding: 0.3em;
|
|
}
|
|
#wrap {
|
|
width: 780px;
|
|
text-align: left;
|
|
margin: 0 auto;
|
|
}
|
|
hr {
|
|
margin: 1em 0;
|
|
color: #C7C7C7;
|
|
background: #C7C7C7;
|
|
border-color: #C7C7C7;
|
|
border-style: none;
|
|
height: 1px;
|
|
}
|
|
h1, h2, h3, h4, h5, h6 {
|
|
font-family: "Trebuchet MS", arial, sans-serif;
|
|
font-weight: bold;
|
|
}
|
|
p {
|
|
text-align: justify;
|
|
}
|
|
</style>
|
|
<TITLE>Manual Page - minimap2(1)</TITLE>
|
|
</HEAD>
|
|
<BODY bgcolor=#F0F0F0 text=#000000 link=#0000ff vlink=#C000C0 alink=#ff0000><div id="wrap"><A NAME=top></A>
|
|
<CENTER>
|
|
<H1><HR><I>Manual Reference Pages - </I><NOBR>minimap2 (1)</NOBR><HR></H1>
|
|
</CENTER>
|
|
<A name=0></A>
|
|
|
|
<H3>NAME</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
<P>
|
|
minimap2 - mapping and alignment between collections of DNA sequences
|
|
</BLOCKQUOTE>
|
|
<A name=contents></A><H3>CONTENTS</H3></A>
|
|
<BLOCKQUOTE>
|
|
<A HREF=#1>Synopsis</A><BR>
|
|
<A HREF=#2>Description</A><BR>
|
|
<A HREF=#3>Options</A><BR>
|
|
<A HREF=#4>Indexing options</A><BR>
|
|
<A HREF=#5>Mapping options</A><BR>
|
|
<A HREF=#6>Alignment options</A><BR>
|
|
<A HREF=#7>Input/output options</A><BR>
|
|
<A HREF=#8>Preset options</A><BR>
|
|
<A HREF=#9>Miscellaneous options</A><BR>
|
|
<A HREF=#10>Output Format</A><BR>
|
|
<A HREF=#11>Limitations</A><BR>
|
|
<A HREF=#12>See Also</A><BR>
|
|
</BLOCKQUOTE>
|
|
<A name=13></A>
|
|
|
|
<H3>SYNOPSIS</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
* Indexing the target sequences (optional):
|
|
<BLOCKQUOTE>
|
|
minimap2
|
|
[<B>-x</B> <I>preset</I>] <B>-d</B> <I>target.mmi</I> <I>target.fa</I> <!-- Need break --><BR>
|
|
minimap2
|
|
[<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>
|
|
<P>
|
|
* Long-read alignment with CIGAR:
|
|
<BLOCKQUOTE>
|
|
minimap2
|
|
<B>-a</B> [<B>-x</B> <I>preset</I>] <I>target.mmi</I> <I>query.fa</I> >
|
|
<I>output.sam</I> <!-- Need break --><BR>
|
|
minimap2
|
|
<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> >
|
|
<I>output.paf</I> </BLOCKQUOTE>
|
|
<P>
|
|
* Long-read overlap without CIGAR:
|
|
<BLOCKQUOTE>
|
|
minimap2
|
|
<B>-x</B> ava-ont
|
|
[<B>-t</B> <I>nThreads</I>] <I>target.fa</I> <I>query.fa</I> >
|
|
<I>output.paf</I> </BLOCKQUOTE>
|
|
</BLOCKQUOTE>
|
|
<A name=2></A>
|
|
|
|
<H3>DESCRIPTION</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
<P>
|
|
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.
|
|
</BLOCKQUOTE>
|
|
<A name=3></A>
|
|
|
|
<H3>OPTIONS</H3>
|
|
|
|
|
|
<BLOCKQUOTE>
|
|
</BLOCKQUOTE>
|
|
<A name=4></A>
|
|
|
|
<H4> Indexing options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-k</B><I> INT</I> </TD><TD valign=bottom>
|
|
Minimizer k-mer length [15]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-w</B><I> INT</I> </TD><TD valign=bottom>
|
|
Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
|
|
in a window of w consecutive k-mers.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-H</B> </TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-I</B><I> NUM</I> </TD><TD valign=bottom>
|
|
Load at most
|
|
<I>NUM</I> target bases into RAM for indexing [4G]. If there are more than
|
|
<I>NUM</I> bases in
|
|
<I>target.fa</I>, minimap2 needs to read
|
|
<I>query.fa</I> multiple times to map it against each batch of target sequences.
|
|
<I>NUM</I> may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
|
|
multi-part index.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--idx-no-seq</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Don’t store target sequences in the index. It saves disk space and memory but
|
|
the index generated with this option will not work with
|
|
<B>-a</B> or
|
|
<B>-c</B>. When base-level alignment is not requested, this option is automatically applied.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-d</B><I> FILE</I> </TD><TD valign=bottom>
|
|
Save the minimizer index of
|
|
<I>target.fa</I> to
|
|
<I>FILE</I> [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
|
|
<B>-H</B>, <B>-k</B>, <B>-w</B>, <B>-I</B> will be effectively overridden by the options stored in the index file.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--alt</B><I> FILE</I> </TD><TD valign=bottom>
|
|
List of ALT contigs [null]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--alt-drop</B><I> FLOAT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Drop ALT hits by
|
|
<I>FLOAT</I> fraction when ranking and computing mapping quality [0.15]
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=5></A>
|
|
|
|
<H4> Mapping options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-f</B><I> FLOAT</I><B>|</B><I>INT1</I><B>[,</B><I>INT2</I><B>]</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
If fraction, ignore top
|
|
<I>FLOAT</I> fraction of most frequent minimizers [0.0002]. If integer,
|
|
ignore minimizers occuring more than
|
|
<I>INT1</I> times.
|
|
<I>INT2</I> is only effective in the
|
|
<B>--sr</B> or
|
|
<B>-xsr</B> mode, which sets the threshold for a second round of seeding.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-U</B><I> INT1</I><B>[,</B><I>INT2</I><B>]</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
|
|
max{<I>INT1</I>, min{<I>INT2</I>, <B>-f</B>}}. This option prevents excessively small or large
|
|
<B>-f</B> estimated from the input reference. Available since r1034 and deprecating
|
|
<B>--min-occ-floor</B> in earlier versions of minimap2.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--q-occ-frac</B><I> FLOAT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Discard a query minimizer if its occurrence is higher than
|
|
<I>FLOAT</I> fraction of query minimizers and than the reference occurrence threshold
|
|
[0.01]. Set 0 to disable. Available since r1105.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-e</B><I> INT</I> </TD><TD valign=bottom>
|
|
Sample a high-frequency minimizer every
|
|
<I>INT</I> basepairs [500].
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-g</B><I> NUM</I> </TD><TD valign=bottom>
|
|
Stop chain enlongation if there are no minimizers within
|
|
<I>NUM</I>-bp [10k].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-r</B><I> NUM1</I><B>[,</B><I>NUM2</I><B>]</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Bandwidth for chaining and base alignment [500,20k].
|
|
<I>NUM1</I> is used for initial chaining and alignment extension;
|
|
<I>NUM2</I> for RMQ-based re-chaining and closing gaps in alignments.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-n</B><I> INT</I> </TD><TD valign=bottom>
|
|
Discard chains consisting of
|
|
<<I>INT</I> number of minimizers [3]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-m</B><I> INT</I> </TD><TD valign=bottom>
|
|
Discard chains with chaining score
|
|
<<I>INT</I> [40]. Chaining score equals the approximate number of matching bases minus a
|
|
concave gap penalty. It is computed with dynamic programming.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-D</B> </TD><TD valign=bottom>
|
|
If query sequence name/length are identical to the target name/length, ignore
|
|
diagonal anchors. This option also reduces DP-based extension along the
|
|
diagonal.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-P</B> </TD><TD valign=bottom>
|
|
Retain all chains and don’t attempt to set primary chains. Options
|
|
<B>-p</B> and
|
|
<B>-N</B> have no effect when this option is in use.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--dual</B>=<B>yes</B>|<B>no</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
If
|
|
<B>no</B>, skip query-target pairs wherein the query name is lexicographically greater
|
|
than the target name [yes]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-X</B> </TD><TD valign=bottom>
|
|
Equivalent to
|
|
’<B>-DP</B> <B>--dual</B>=<B>no</B> <B>--no-long-join</B>’. Primarily used for all-vs-all read overlapping.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-p</B><I> FLOAT</I> </TD><TD valign=bottom>
|
|
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
|
|
Between two chains overlaping over half of the shorter chain (controlled by
|
|
<B>-M</B>), the chain with a lower score is secondary to the chain with a higher score.
|
|
If the ratio of the scores is below
|
|
<I>FLOAT</I>, the secondary chain will not be outputted or extended with DP alignment later.
|
|
This option has no effect when
|
|
<B>-X</B> is applied.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-N</B><I> INT</I> </TD><TD valign=bottom>
|
|
Output at most
|
|
<I>INT</I> secondary alignments [5]. This option has no effect when
|
|
<B>-X</B> is applied.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-G</B><I> NUM</I> </TD><TD valign=bottom>
|
|
Maximum gap on the reference (effective with
|
|
<B>-xsplice</B>/<B>--splice</B>). This option also changes the chaining and alignment band width to
|
|
<I>NUM</I>. Increasing this option slows down spliced alignment. [200k]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-F</B><I> NUM</I> </TD><TD valign=bottom>
|
|
Maximum fragment length (aka insert size; effective with
|
|
<B>-xsr</B>/<B>--frag</B>=<B>yes</B>) [800]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-M</B><I> FLOAT</I> </TD><TD valign=bottom>
|
|
Mark as secondary a chain that overlaps with a better chain by
|
|
<I>FLOAT</I> or more of the shorter chain [0.5]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--rmq</B>=<B>no</B>|<B>yes</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
|
|
for aligning contigs through long INDELs.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--hard-mask-level</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Honor option
|
|
<B>-M</B> and disable a heurstic to save unmapped subsequences and disables
|
|
<B>--mask-len</B>. </TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--mask-len</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Keep an alignment if dropping it leaves an unaligned region on query longer than
|
|
<I>INT</I> [inf]. Effective without
|
|
<B>--hard-mask-level</B>. </TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--max-chain-skip</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
A heuristics that stops chaining early [25]. 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
|
|
<I>INT</I> to a large number to switch off this heurstics.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--max-chain-iter</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Check up to
|
|
<I>INT</I> partial chains during chaining [5000]. This is a heuristic to avoid quadratic
|
|
time complexity in the worst case.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--chain-gap-scale</B><I> FLOAT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Scale of gap cost during chaining [1.0]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--no-long-join</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Disable the long gap patching heuristic. When this option is applied, the
|
|
maximum alignment gap is mostly controlled by
|
|
<B>-r</B>. </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--splice</B> </TD><TD valign=bottom>
|
|
Enable the splice alignment mode.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--sr</B> </TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--split-prefix</B><I> STR</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Prefix to create temporary files. Typically used for a multi-part index.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--frag</B>=<B>no</B>|<B>yes</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Whether to enable the fragment mode [no]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--for-only</B> </TD><TD valign=bottom>
|
|
Only map to the forward strand of the reference sequences. For paired-end
|
|
reads in the forward-reverse orientation, the first read is mapped to forward
|
|
strand of the reference and the second read to the reverse stand.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--rev-only</B> </TD><TD valign=bottom>
|
|
Only map to the reverse complement strand of the reference sequences.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--heap-sort</B>=<B>no</B>|<B>yes</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
|
|
faster for short reads, but slower for long reads. [no]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--no-pairing</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Treat two reads in a pair as independent reads. The mate related fields in SAM
|
|
are still properly populated.
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=6></A>
|
|
|
|
<H4> Alignment options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-A</B><I> INT</I> </TD><TD valign=bottom>
|
|
Matching score [2]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-B</B><I> INT</I> </TD><TD valign=bottom>
|
|
Mismatching penalty [4]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-O</B><I> INT1[,INT2]</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Gap open penalty [4,24]. If
|
|
<I>INT2</I> is not specified, it is set to
|
|
<I>INT1</I>. </TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-E</B><I> INT1[,INT2]</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Gap extension penalty [2,1]. A gap of length
|
|
<I>k</I> costs
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-C</B><I> INT</I> </TD><TD valign=bottom>
|
|
Cost for a non-canonical GT-AG splicing (effective with
|
|
<B>--splice</B>) [0]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>-z</B><I> INT1[,INT2]</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Truncate an alignment if the running alignment score drops too quickly along
|
|
the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the
|
|
drop of score is above
|
|
<I>INT2</I>, minimap2 will reverse complement the query in the related region and align
|
|
again to test small inversions. Minimap2 truncates alignment if there is an
|
|
inversion or the drop of score is greater than
|
|
<I>INT1</I>. Decrease
|
|
<I>INT2</I> to find small inversions at the cost of performance and false positives.
|
|
Increase
|
|
<I>INT1</I> to improves the contiguity of alignment at the cost of poor alignment in the
|
|
middle.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-s</B><I> INT</I> </TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-u</B><I> CHAR</I> </TD><TD valign=bottom>
|
|
How to find canonical splicing sites GT-AG -
|
|
<B>f</B>: transcript strand;
|
|
<B>b</B>: both strands;
|
|
<B>n</B>: no attempt to match GT-AG [n]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--end-bonus</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Score bonus when alignment extends to the end of the query sequence [0].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--score-N</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Score of a mismatch involving ambiguous bases [1].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--splice-flank</B>=<B>yes</B>|<B>no</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Assume the next base to a
|
|
<B>GT</B> donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
|
|
base to a
|
|
<B>AG</B> acceptor tends to be C/T [no].
|
|
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
|
|
<B>--splice</B>. 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
|
|
<B>--splice-flank=no</B> to the command line.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--junc-bed</B> FILE </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Gene annotations in the BED12 format (aka 12-column BED), or intron positions
|
|
in 5-column BED. With this option, minimap2 prefers splicing in annotations.
|
|
BED12 file can be converted from GTF/GFF3 with ‘paftools.js gff2bed anno.gtf’
|
|
[].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--junc-bonus</B> INT </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Score bonus for a splice donor or acceptor found in annotation (effective with
|
|
<B>--junc-bed</B>) [9].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--end-seed-pen</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Drop a terminal anchor if
|
|
<I>s</I><log(<I>g</I>)+<I>INT</I>, where
|
|
<I>s</I> is the local alignment score around the anchor and
|
|
<I>g</I> the length of the terminal gap in the chain. This option is only effective
|
|
with
|
|
<B>--splice</B>. It helps to avoid tiny terminal exons. [6]
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--no-end-flt</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Don’t filter seeds towards the ends of chains before performing base-level
|
|
alignment.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--cap-sw-mem</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Skip alignment if the DP matrix size is above
|
|
<I>NUM</I>. Set 0 to disable [100m].
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--cap-kalloc</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
|
|
<I>NUM</I>. Set 0 to disable [0].
|
|
</TD></TR>
|
|
<TR></TR></TABLE></BLOCKQUOTE>
|
|
<A name=7></A>
|
|
|
|
<H4> Input/output options</H4>
|
|
|
|
<BLOCKQUOTE>
|
|
<TABLE cellpadding=3>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-a</B> </TD><TD valign=bottom>
|
|
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
|
|
by default.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-o</B><I> FILE</I> </TD><TD valign=bottom>
|
|
Output alignments to
|
|
<I>FILE</I> [stdout].
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-Q</B> </TD><TD valign=bottom>
|
|
Ignore base quality in the input file.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-L</B> </TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-R</B><I> STR</I> </TD><TD valign=bottom>
|
|
SAM read group line in a format like
|
|
<B>@RG\\tID:foo\\tSM:bar</B> [].
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-y</B> </TD><TD valign=bottom>
|
|
Copy input FASTA/Q comments to output.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-c</B> </TD><TD valign=bottom>
|
|
Generate CIGAR. In PAF, the CIGAR is written to the ‘cg’ custom tag.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--cs[=</B><I>STR</I><B>]</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Output the
|
|
<B>cs</B> tag.
|
|
<I>STR</I> can be either
|
|
<I>short</I> or
|
|
<I>long</I>. If no
|
|
<I>STR</I> is given,
|
|
<I>short</I> is assumed. [none]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--MD</B> </TD><TD valign=bottom>
|
|
Output the MD tag (see the SAM spec).
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--eqx</B> </TD><TD valign=bottom>
|
|
Output =/X CIGAR operators for sequence match/mismatch.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-Y</B> </TD><TD valign=bottom>
|
|
In SAM output, use soft clipping for supplementary alignments.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>--seed</B><I> INT</I> </TD><TD valign=bottom>
|
|
Integer seed for randomizing equally best hits. Minimap2 hashes
|
|
<I>INT</I> and read name when choosing between equally best hits. [11]
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-t</B><I> INT</I> </TD><TD valign=bottom>
|
|
Number of threads [3]. Minimap2 uses at most three threads when indexing target
|
|
sequences, and uses up to
|
|
<I>INT</I>+1 threads when mapping (the extra thread is for I/O, which is frequently idle and
|
|
takes little CPU time).
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>-2</B> </TD><TD valign=bottom>
|
|
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.
|
|
</TD></TR>
|
|
<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 colspan=2>
|
|
<B>--max-qlen</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
Filter out query sequences longer than
|
|
<I>NUM</I>. </TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--paf-no-hit</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
In PAF, output unmapped queries; the strand and the reference name fields are
|
|
set to ‘*’. Warning: some paftools.js commands may not work with such output
|
|
for the moment.
|
|
</TD></TR>
|
|
<TR valign=top><TD colspan=2>
|
|
<B>--sam-hit-only</B> </TD></TR><TR valign=top><TD width=10%> </TD><TD>
|
|
In SAM, don’t output unmapped reads.
|
|
</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=10% nowrap>
|
|
<B>map-ont</B> </TD><TD valign=bottom>
|
|
Align noisy long reads of ~10% error rate to a reference genome. This is the
|
|
default mode.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>map-hifi</B> </TD><TD valign=bottom>
|
|
Align PacBio high-fidelity (HiFi) reads to a reference genome
|
|
(<B>-k19</B> <B>-w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1</B> <B>-s200</B>). </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>map-pb</B> </TD><TD valign=bottom>
|
|
Align older PacBio continuous long (CLR) reads to a reference genome
|
|
(<B>-Hk19</B>). </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>asm5</B> </TD><TD valign=bottom>
|
|
Long assembly to reference mapping
|
|
(<B>-k19</B> <B>-w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200</B> <B>-N50</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=10% nowrap>
|
|
<B>asm10</B> </TD><TD valign=bottom>
|
|
Long assembly to reference mapping
|
|
(<B>-k19</B> <B>-w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200</B> <B>-N50</B>). Up to 10% sequence divergence.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>asm20</B> </TD><TD valign=bottom>
|
|
Long assembly to reference mapping
|
|
(<B>-k19</B> <B>-w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200</B> <B>-N50</B>). Up to 20% sequence divergence.
|
|
</TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>splice</B> </TD><TD valign=bottom>
|
|
Long-read spliced alignment
|
|
(<B>-k15</B> <B>-w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0</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=10% nowrap>
|
|
<B>splice:hq</B> </TD><TD valign=bottom>
|
|
Long-read splice alignment for PacBio CCS reads
|
|
(<B>-xsplice</B> <B>-C5 -O6,24</B> <B>-B4</B>). </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>sr</B> </TD><TD valign=bottom>
|
|
Short single-end reads without splicing
|
|
(<B>-k21</B> <B>-w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20</B> <B>-s40 -g100 -2K50m --heap-sort=yes</B> <B>--secondary=no</B>). </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>ava-pb</B> </TD><TD valign=bottom>
|
|
PacBio CLR all-vs-all overlap mapping
|
|
(<B>-Hk19</B> <B>-Xw5 -e0</B> <B>-m100</B>). </TD></TR>
|
|
<TR valign=top><TD width=10% nowrap>
|
|
<B>ava-ont</B> </TD><TD valign=bottom>
|
|
Oxford Nanopore all-vs-all overlap mapping
|
|
(<B>-k15</B> <B>-Xw5 -e0 -m100</B> <B>-r2k</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,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>MD</TD><TD align=center>Z</TD><TD>To generate the ref sequence 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>SA</TD><TD align=center>Z</TD><TD>List of other supplementary alignments</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>
|
|
<TR valign=top>
|
|
<TD align=right>dv</TD><TD align=center>f</TD><TD>Approximate per-base sequence divergence</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>de</TD><TD align=center>f</TD><TD>Gap-compressed per-base sequence divergence</TD></TR>
|
|
<TR valign=top>
|
|
<TD align=right>rl</TD><TD align=center>i</TD><TD>Length of query regions harboring repetitive seeds</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 or NEON instructions to compile. It is possible to add
|
|
non-SSE2/NEON 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>minimap2-2.23 (r1111)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>18 November 2021</I></TD> </TR></TABLE></div></BODY></HTML>
|