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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?
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?
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