Scaffolder help

[dbrami]

Hi folks,

I am trying to scaffold some sequences I have in a 'contigs.fasta' file.
The contigs range in size from 1k to 37k.
I have tried using the scaffolding portion of the SOAPdeNovo; it can't seem to map any of my reads back to my assembly, so this doesn't work.

I have tried using BAMBUS2 but it is telling me "No library account found in bank XYZ". I would have loved to use its option of using a closely related sequence for scaffolding...

Finally, I have tried SSPACE. It mapped a very small portion of reads and extended another few contigs, but there has been no real progress made with this one, but at least it completed.

Oddly enough, a BWA mapping of my reads to contigs shows a beautiful and deep coverage almost everywhere. Ideally, I would have substituted the Bowtie alignments from SSPACE for my SAM/BAM file but I don't have access to the premium version of SSPACE.

Does anyone have any suggestions?

[boetsie]

Hi dbrami,

what is the type of the sequences you have? Paired-end? And what size?

Did you try to map the sequences yourself using Bowtie?

Regards,
Boetsie

Hi folks,

I am trying to scaffold some sequences I have in a 'contigs.fasta' file.
The contigs range in size from 1k to 37k.
I have tried using the scaffolding portion of the SOAPdeNovo; it can't seem to map any of my reads back to my assembly, so this doesn't work.

I have tried using BAMBUS2 but it is telling me "No library account found in bank XYZ". I would have loved to use its option of using a closely related sequence for scaffolding...

Finally, I have tried SSPACE. It mapped a very small portion of reads and extended another few contigs, but there has been no real progress made with this one, but at least it completed.

Oddly enough, a BWA mapping of my reads to contigs shows a beautiful and deep coverage almost everywhere. Ideally, I would have substituted the Bowtie alignments from SSPACE for my SAM/BAM file but I don't have access to the premium version of SSPACE.

Does anyone have any suggestions?