I have an hybrid contigs of 454 + Illumina + SOLiD which is around 850 Mb. Now I want to create scaffolds using SSPACE with 20kb (3 libraries) of 454 paired end reads which have been converted into Paired end fastq reads (linker were removed).
Can anyone help me out with this or suggest some better approach for scaffolding?
Sorry, I do not understand this question, there are confused indications and too many short names
I want to do scaffolding with SSPACE using paired end (20kb) reads of Roche 454.
I used SSPAce for the scaffolding of bacterial genomes. What are your difficulties at this time of your analysis?
SSPACE worked well for my analysis, but it was for small genomes.
My guess is that you will have to extract the reads with the pair-end linker sequence from your 20kb sff file. Then create read1 and read2 fastq files and then use them with SSPACE. Have you already figured out how to do this? Please do share.
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