building scaffolds using a contig and mate pair

[boetsie]

I believe CLCBio export assemblies as ace file.

For large datasets, somehow no .ace files are produced.

[mack]

I believe CLCBio export assemblies as ace file.

[boetsie]

any updates on this....

well, not yet. We also had the problem that we couldn't generate an .ace file for Bambus. We are currently working on a script for this problem, since none of the existing programs today can do this.

[gabriel.lichtenstein]

any updates on this....

[boetsie]

Thanks for the reply's, but I don't think you answers work..

MIRA uses Bambus for scaffolding (if i'm correct?).
Though, Bambus doesn't read in a .fasta file for scaffolding, it needs a .contig file, which i don't have. In addition, i can't put in the two mate-pair files i have (one for each read end), only a regular expression of how the two pairs are mated.

So, my input is;

- 1 .fasta file containing contigs
- 2 .fasta files containing the mate pairs

Is there a way to do this?

Kind regards,
Marten

[[email protected]]

Hi all,

We are currently performing a de novo assembly using Illumina mate-pairs. we have assembled them using CLCBio, though with CLCBio no scaffolds can be produced, only contigs. Now we have mate pairs, so we would like to use them to make a scaffold.

The problem is that assembly programs like SOAPdenovo or SSAke etc. use files which where produced during contig assembling. They don't have a stand-alone program for just scaffolding a contig file.

Is there any software/algorithm available which has the contigs file (in .fasta format) and mate pair files as input, and can produce a scaffold? Or has someone a solution?

Kind regards,
Marten

Marten, you can use Bambus 2.33 by AMOS. It takes contig and mate file as input. I am also trying to use it but i dont have mate file as required by Bambus. DO you know how to create mate file? I have paired end reads from illumina

[Zigster]

I'm pretty sure MIRA can do that. Set aside a couple days to read the manual though (it is very long)

[boetsie]

Hi all,

We are currently performing a de novo assembly using Illumina mate-pairs. we have assembled them using CLCBio, though with CLCBio no scaffolds can be produced, only contigs. Now we have mate pairs, so we would like to use them to make a scaffold.

The problem is that assembly programs like SOAPdenovo or SSAke etc. use files which where produced during contig assembling. They don't have a stand-alone program for just scaffolding a contig file.

Is there any software/algorithm available which has the contigs file (in .fasta format) and mate pair files as input, and can produce a scaffold? Or has someone a solution?

Kind regards,
Marten