[ngs] bwa mem vs aln + sampe

[Rayan Chikhi]

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).
See http://bio-bwa.sourceforge.net/bwa.shtml#2
I think it is fair to say that mem should replace aln/sampe for everything
now. (except maybe on older, < 70 bp reads)

Rayan

On Tue, Jun 25, 2013 at 1:48 PM, Cox, Allison J <allison-cox at uiowa.edu>wrote:

> Hi all,
> Is there a difference between using the single mem command vs. first aln
> and then sampe in BWA?
> Thanks,
> Allison
>
> On 6/24/13 10:04 AM, "C. Titus Brown" <ctb at msu.edu> wrote:
>
> >Hi all,
> >
> >here is the list of names & e-mail addresses for all y'all:
> >
> >
> https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidGRkNHZjMXFwcmRZT
> >0trZTlmVkZKcFE#gid=0
> >
> >cheers,
> >--titus
> >--
> >C. Titus Brown, ctb at msu.edu
> >
> >_______________________________________________
> >ngs-2013 mailing list
> >ngs-2013 at lists.idyll.org
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