Re: [Samtools-devel] Any assemblers accept the SAM format as input yet?

[Aylwyn S. <as...@sa...>]

On Wed, 25 Mar 2009, Heng Li wrote:

> Hello Thon,
>
> I think you are talking about local de novo assembly around structural 
> variations. SAM is designed with this application in mind. It puts unmapped 
> mate close to the mapped mate and therefore retrieving data for local 
> assembly is convenient and highly efficient.
>
> Aylwyn from Richard's group has a pipeline to do such local de novo assembly 
> based on maq's output. I guess it is straightforward to adapt the pipeline to 
> SAM when this is really needed in future. So far as I know, all the standard 
> de novo assemblers take a fastq or a fasta file as the input. You have to 
> develop a pipeline to feed data to them.

That's correct. I have considered adapting to use the SAM format as it 
would actually be somewhat more convenient than the Maq map format. So I 
would say SAM is a good format for use in assembly.

Aylwyn

> Heng
>
> On 24 Mar 2009, at 23:33, Complete Genomics Developer Support wrote:
>
>> Hi,
>> 
>> Are there any assemblers that use the SAM/BAM output as input yet?
>> As I see it, the SAM file is an intermediate step between mapping and 
>> assembly, since assembly of the complete sequence to facilitate proper 
>> variation calling requires the de-novo assembly of reads that did not 
>> initially map to the reference, but which have a consistent mate pair some 
>> distance away?I understand that samtools is not attempting to do any of 
>> these types of assembly, but maybe others do?
>> 
>> We are looking for a format that can represent the mapping of our read 
>> structure, but also that would be able to be used as the input format for 
>> downstream assembly. We expect that many of our customers would want to 
>> independently verify our assembly to other assemblies.
>> 
>> Thanks,
>> 
>> Thon
>> __________________________________
>> Thon de Boer, Ph.D.
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>> Complete Genomics, Inc.
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