/usr/share/doc/last-align/last-tuning.html

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<div class="document" id="last-performance-tuning">
<h1 class="title">LAST Performance Tuning</h1>

<p>This document tells you how to make LAST <strong>faster</strong>, at a cost in
sensitivity or memory use, or <strong>more sensitive</strong>, at a cost in speed.</p>
<p>Ideally, the default settings would always work well.  Unfortunately,
there is too great a variety of challenging alignment tasks, and the
LAST developers lack experience with most of them.</p>
<p>LAST must have <em>some</em> defaults, and any choice will displease someone.
It is wrong to say &quot;LAST is faster but less sensitive than method X&quot;,
or &quot;slower but more sensitive than method Y&quot;, without varying the
defaults.</p>
<div class="section" id="lastdb-w">
<h2>lastdb -w</h2>
<p>This option <strong>reduces memory and disk usage</strong>.  It makes lastdb and
probably lastal <strong>faster</strong>.  By default lastdb indexes every position
in the sequence(s), but -w2 makes it index every 2nd position, -w3
every 3rd position, etc.  This may <strong>reduce sensitivity</strong>, but not
necessarily, because LAST uses initial matches that are sufficiently
rare, and by ignoring some matches the remaining ones become rarer.</p>
<p>Among other aligners, MegaBLAST indexes every 5th position, and BLAT
indexes every 11th position.</p>
</div>
<div class="section" id="lastdb-i">
<h2>lastdb -i</h2>
<p>This option <strong>makes lastdb faster</strong>, but disables some lastal options.
If lastdb is too slow, try -i10.</p>
</div>
<div class="section" id="lastdb-c">
<h2>lastdb -C</h2>
<p>This option may make lastal a bit <strong>faster</strong>, but <strong>uses more memory
and disk</strong>, and makes lastdb slower.  If these downsides are no
problem, you may as well try it.  -C3 is fastest (at least sometimes)
but uses most memory, -C2 is almost as fast.</p>
</div>
<div class="section" id="lastal-m">
<h2>lastal -m</h2>
<p>This option <strong>trades speed for sensitivity</strong>.  It sets the rareness
limit for initial matches: initial matches are lengthened until they
occur at most this many times in the lastdb volume.  The default is
10.  So -m100 makes it more sensitive but slower, by using more
initial matches.</p>
</div>
<div class="section" id="lastal-l">
<h2>lastal -l</h2>
<p>This option makes lastal <strong>faster</strong> but <strong>less sensitive</strong>.  It sets
the minimum length of initial matches, e.g. -l50 means length 50.
(The default is 1).  This can make it <em>much</em> faster, and the
sensitivity is adequate if the alignments contain long, gapless,
high-identity matches.</p>
</div>
<div class="section" id="lastal-k">
<h2>lastal -k</h2>
<p>This option makes lastal <strong>faster</strong> but <strong>less sensitive</strong>.  By
default lastal looks for initial matches starting at every position in
the query sequence(s), but -k2 makes it check every 2nd position, -k3
every 3rd position, etc.  Be careful about combining this with lastdb
option -w.</p>
</div>
<div class="section" id="lastal-x">
<h2>lastal -x</h2>
<p>This option can make lastal <strong>faster</strong> but <strong>less sensitive</strong>.  It
sets the maximum score drop in alignments, in the gapped extension
phase.  Lower values make it faster, by quitting unpromising
extensions sooner.  The default aims at best accuracy.</p>
<p>Unfortunately, the default is a complex function of the other
parameters and the database size.  You can see it in the lastal header
after &quot;x=&quot;, e.g. by running lastal with no queries.  Then try, say,
halving it.</p>
</div>
<div class="section" id="lastal-c">
<h2>lastal -C</h2>
<p>This option (gapless alignment culling) can make lastal <strong>faster</strong> but
<strong>less sensitive</strong>.  It can also <strong>reduce redundant output</strong>.  For
example, -C2 makes it discard alignments (before gapped extension)
whose query coordinates lie in those of 2 or more stronger alignments.</p>
</div>
<div class="section" id="lastal-j1">
<h2>lastal -j1</h2>
<p>This option requests <strong>gapless</strong> alignment, which is <strong>faster</strong>.  (You
could get the same effect by using very high gap costs, but -j1 is
faster because it skips the gapping phase entirely.)</p>
</div>
<div class="section" id="lastal-f">
<h2>lastal -f</h2>
<p>Option -fTAB <strong>reduces the output size</strong>, which can improve speed.</p>
</div>
<div class="section" id="repeat-masking">
<h2>Repeat masking</h2>
<p>This can make LAST <strong>much faster</strong>, produce <strong>less output</strong>, and
reduce memory and disk usage.  Please see <a class="reference external" href="last-repeats.html">last-repeats.html</a>.</p>
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last-align 712-1ubuntu1 / usr / share / doc / last-align / last-tuning.html
