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 <andr...@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. > > -- > http://fam-tille.de > > > -- > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: http://lists.debian.org/20110401155534.gl22...@an3as.eu > > -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/AANLkTin�0wtkfyecncf26+bxpuidudz904bg8tg...@mail.gmail.com
