Re: ensembl_57-7_amd64.changes ACCEPTED into experimental
I will ask about ssaha2 and i will follow with a letter similar to the
soapdenovo one. as i said we got sanger and ebi people here.
while we are suggesting packages, have you guys seen this tool?
http://sourceforge.net/apps/mediawiki/denovoassembler/index.php?title=Main_Page
NGE sequencer using MPI (which means i can link it against Platform LSF MPI)
On Fri, Apr 1, 2011 at 6:55 PM, Andreas Tille <andreas@an3as.eu> wrote:
> On Fri, Apr 01, 2011 at 03:44:07PM +0100, William Spooner wrote:
>> Sadly SSAHA2 uses crossmatch, which is non-free,
>
> I have no idea about crossmatch but I'm always a fan of simply asking
> whether something could be relased under a free license or not. As long
> as nobody asks the authors will not considering to release. So has
> somebody just asked? (I'm sorry if this question is quite naive - but I
> had about 25-30% success when just trying ...)
>
>> meaning SSAHA2 is not appropriate for debian-med. I can get you the source for ssaha, but it's so old now that I doubt anyone would still want to use it.
>
> I know where to find this source and we just agreed here that plain old
> ssaha is not worth spending much time into it.
>
>> The latest tool from the same group is called SMALT - this is probably worth perusing. I believe that it uses the same k-mer index table algorithm as SSAHA (and BLAT); i.e. is a different algorithm to the Burrows-Wheeler tools that are so popular in the short-read world.
>>
>> http://www.sanger.ac.uk/resources/software/smalt/
>
> Just added to the tasks file - thanks for the hint
>
> Andreas.
>
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