[ngs] bwa mem vs aln + sampe

liz wright lzwright at gmail.com
Wed Jun 26 12:37:10 PDT 2013


further justification for BWA mem
http://www.bioplanet.com/gcat/reports/80/alignment/250bp-pe-small-indel/bwa/compare-68-72


On Tue, Jun 25, 2013 at 2:04 PM, Rayan Chikhi <rchikhi at gmail.com> wrote:

> 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
>> >
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>>
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>
>
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