<div dir="ltr">further justification for BWA mem <a href="http://www.bioplanet.com/gcat/reports/80/alignment/250bp-pe-small-indel/bwa/compare-68-72">http://www.bioplanet.com/gcat/reports/80/alignment/250bp-pe-small-indel/bwa/compare-68-72</a></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jun 25, 2013 at 2:04 PM, Rayan Chikhi <span dir="ltr"><<a href="mailto:rchikhi@gmail.com" target="_blank">rchikhi@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes, the aln/sampe commands invoke the original BWA algorithm (backtracking, from 2009), and the mem command invokes the latest BWA improvement (MEM algorithm, 2013). <br>See <a href="http://bio-bwa.sourceforge.net/bwa.shtml#2" target="_blank">http://bio-bwa.sourceforge.net/bwa.shtml#2</a><br>
I think it is fair to say that mem should replace aln/sampe for everything now. (except maybe on older, < 70 bp reads)<span class="HOEnZb"><font color="#888888"><br><br>Rayan</font></span><div class="HOEnZb"><div class="h5">
<br><br><div class="gmail_quote">
On Tue, Jun 25, 2013 at 1:48 PM, Cox, Allison J <span dir="ltr"><<a href="mailto:allison-cox@uiowa.edu" target="_blank">allison-cox@uiowa.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
Is there a difference between using the single mem command vs. first aln<br>
and then sampe in BWA?<br>
Thanks,<br>
Allison<br>
<br>
On 6/24/13 10:04 AM, "C. Titus Brown" <<a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a>> wrote:<br>
<br>
>Hi all,<br>
><br>
>here is the list of names & e-mail addresses for all y'all:<br>
><br>
><a href="https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidGRkNHZjMXFwcmRZT" target="_blank">https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidGRkNHZjMXFwcmRZT</a><br>
>0trZTlmVkZKcFE#gid=0<br>
><br>
>cheers,<br>
>--titus<br>
>--<br>
>C. Titus Brown, <a href="mailto:ctb@msu.edu" target="_blank">ctb@msu.edu</a><br>
><br>
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