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updated the manpage

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Heng Li
2021-06-26 19:29:14 -04:00
parent 870f2cc2b9
commit 81b3da7677
1 changed files with 56 additions and 50 deletions
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@@ -216,20 +216,27 @@ ignore minimizers occuring more than
<B>-xsr</B> mode, which sets the threshold for a second round of seeding.
</TD></TR>
<TR valign=top><TD colspan=2>
<B>--min-occ-floor</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Force minimap2 to always use k-mers occurring
<I>INT</I> times or less [0]. In effect, the max occurrence threshold is set to
the
max{<I>INT</I>, <B>-f</B>}. </TD></TR>
<TR valign=top><TD width=10% nowrap>
<B>-g</B><I> INT</I> </TD><TD valign=bottom>
Stop chain enlongation if there are no minimizers within
<I>INT</I>-bp [10000].
<B>-U</B><I> INT1</I><B>[,</B><I>INT2</I><B>]</B> </TD></TR><TR valign=top><TD width=10%>&nbsp;</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. It deprecates
<B>--min-occ-floor</B> in earlier versions of minimap2.
</TD></TR>
<TR valign=top><TD width=10% nowrap>
<B>-r</B><I> INT</I> </TD><TD valign=bottom>
Bandwidth used in chaining and DP-based alignment [500]. This option
approximately controls the maximum gap size.
<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%>&nbsp;</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>
@@ -298,6 +305,11 @@ 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%>&nbsp;</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%>&nbsp;</TD><TD>
Honor option
<B>-M</B> and disable a heurstic to save unmapped subsequences and disables
@@ -330,11 +342,6 @@ Scale of gap cost during chaining [1.0]
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 colspan=2>
<B>--lj-min-ratio</B><I> FLOAT</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Fraction of query sequence length required to bridge a long gap [0.5]. A
smaller value helps to recover longer gaps, at the cost of more false gaps.
</TD></TR>
<TR valign=top><TD width=10% nowrap>
<B>--splice</B> </TD><TD valign=bottom>
Enable the splice alignment mode.
@@ -483,7 +490,7 @@ alignment.
<TR valign=top><TD colspan=2>
<B>--cap-sw-mem</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Skip alignment if the DP matrix size is above
<I>NUM</I>. Set 0 to disable [0].
<I>NUM</I>. Set 0 to disable [100m].
</TD></TR>
<TR></TR></TABLE></BLOCKQUOTE>
<A name=7></A>
@@ -614,61 +621,60 @@ values set by
<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>
<TR valign=top><TD width=10% 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.
Align noisy long reads of ~10% error rate to a reference genome. This is the
default mode.
</TD></TR>
<TR valign=top><TD width=8% nowrap>
<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 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50</B> <B>--min-occ-floor=100</B>). Typically, the alignment will not extend to regions with 5% or higher sequence
(<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=8% nowrap>
<TR valign=top><TD width=10% 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 -z200 -N50</B> <B>--min-occ-floor=100</B>). Up to 10% sequence divergence.
(<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=8% nowrap>
<TR valign=top><TD width=10% nowrap>
<B>asm20</B> </TD><TD valign=bottom>
Long assembly to reference mapping
(<B>-k19</B> <B>-w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50</B> <B>--min-occ-floor=100</B>). Up to 20% sequence divergence.
(<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=8% nowrap>
<B>ava-pb</B> </TD><TD valign=bottom>
PacBio all-vs-all overlap mapping
(<B>-Hk19</B> <B>-Xw5 -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>-Xw5 -m100 -g10000 -r2000 --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>
<TR valign=top><TD width=10% 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 --junc-bonus=9</B> <B>--splice-flank=yes</B>). In the splice mode, 1) long deletions are taken as introns and represented as
(<B>-k15</B> <B>-w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -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
&#145;<B>N</B>&#146; CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the
&#145;<B>ms</B>&#146; tag ignores introns to demote hits to pseudogenes.
</TD></TR>
<TR valign=top><TD colspan=2>
<B>splice:hq</B> </TD></TR><TR valign=top><TD width=8%>&nbsp;</TD><TD>
<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=8% nowrap>
<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 -r50 -p.5 -N20 -f1000,5000 -n2 -m20</B> <B>-s40 -g200 -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>
@@ -831,4 +837,4 @@ non-SSE2/NEON support, but it would make minimap2 slower by several times.
miniasm(1), minimap(1), bwa(1).
</BLOCKQUOTE>
<P><HR>
<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.18 (r1015)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>9 April 2021</I></TD> </TR></TABLE></div></BODY></HTML>
<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.20 (r1061)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>27 May 2021</I></TD> </TR></TABLE></div></BODY></HTML>