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<html><head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
<link href="faq_files/velvetmem.css" rel="stylesheet" type="text/css">
<link rel="stylesheet" type="text/css" href="faq_files/main.css">
<!--<script src="scripts/velvetmem.js" type="text/javascript"></script>-->
<title>VelvetMem Ajax Caculator-Important Notes</title>
</head><body>
<div id="header" style="font-size: 9pt;">
<h1>Important Notes</h1>
</div>
<span style="font: status-bar; font-size: 8pt;">Simon Gladman,
Torsten Seemann ,Middha, Kevin Lam, Zigster, jGibbons, Francesco Vezzi,
Leonardo Varuzza, Jacob Israel.</span>
<p style="font: status-bar;">
The formula derived by Simon Gladman has a caveat of only being
applicable to Velvet when compiled with the default <b>MAXKMERSIZE=31</b>.
If you compiled with 63 for example, the memory usage will increase.
<br><br>
<b>So what happens when the machine doesn't have enough ram?</b>
<br>
It will segfault, but sometimes it will lock up a machine so badly you
will have to physically pull the plug.using ulimit, for example I have a
256gb machine and use ulimit -v 240000000 before every run
<br><br>
<b>The regression equation should be fairly valid for the following
ranges:</b>
<br>
K(velvet parameter) = 15 - 31.<br>
Numreads = 5 - 70 million. <br>
Genome size = 2 - 10 Megabases. <br>
Read length (size) = 20 - 75 bases. <br>
<br><br>
This faq page will be updated as soon as possible.
</p>
</body></html>