Re: [AMOS-help] scaffold contigs in fasta format using mate pair

[Dan B. <dan...@gm...>]

On 16 December 2010 15:35, Marten Boetzer <mbo...@ho...> wrote:
> Hi Dan,
>
> i've developed my own scaffolder called SSPACE, it is accepted for
> publication in Bioinformatics and the paper will be online soon. Please have
> a look at this thread;
>
> http://seqanswers.com/forums/showthread.php?t=8350&highlight=SSPACE

Thanks Marten,

That is certainly an interesting development!


Dan.


> where is a link for downloading the tool.
>
> Cheers,
> Marten
>
>> Date: Thu, 16 Dec 2010 14:25:22 +0000
>> Subject: Re: [AMOS-help] scaffold contigs in fasta format using mate pair
>> From: dan...@gm...
>> To: mbo...@ho...
>> CC: amo...@li...
>>
>> This should be possible by turning your files into a format recognised
>> by Bambus. Sorry, did you get a reply already? If not, can you explain
>> the format of your mate pair information, and then we can work out how
>> to convert it into a GFD-like .contig file for input to Bambus.
>>
>>
>>
>> On 25 February 2010 12:21, Marten Boetzer <mbo...@ho...> wrote:
>> > Hello,
>> >
>> > i have a problem. We used a program that can build contigs, but can't
>> > build
>> > scaffolds. Therefore, we are searching for a stand-alone program for
>> > scaffolding. We came to Bambus, but we didn't find our problem in the
>> > manual. Any additional files, besides the .fasta file of the contigs, we
>> > don't have.
>> >
>> > Is it possible to put in a .fasta file containing the contigs and then
>> > scaffold these contigs using 2 mate-pair files?
>> >
>> > Kind regards,
>> >
>> > Marten Boetzer
>> >
>> >
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