Hi all, I was just wondering if this would be a legitimate strategy before putting in a lot of effort. Or if it's been done before.
I have a many, many single end runs of Illumina. Most are 1x70bp. I was thinking that if I split each of the raw reads into a 2x35 set, then maybe a scaffolder like SOPRA could help me bridge gaps. Is this crazy? If it's not crazy, are there any recommendations?
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Lee Katz
Aggree with Leszek. Don't invest any time into this. To understand why, imagine the answers to following questions:
I agree with Leszek in that you would need longer reads for this approach to be useful. However, I am skeptical about whether splitting up long reads into fake pairs would improve things more than just assembling with the long reads, but I think it is worth investigating. This approach is described in How Can I Do Scaffolding With The Single End Data ? to a similar question (and I think my comment to that answer has some things worth considering).
Ah, on some of the genomes, there are 454 reads. A comment in that discussion by the developer of SSPACE says that it might provide some useful information.
However, most comments in this thread and that thread are pretty convincing that there will be no useful information added in virtually all cases. I might not continue with this.
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why do you want to do additional scaffolding? is your assembly fragmented?
Forgive my ignorance here, but how is breaking down a read into two 35 bp regions without a gap different than using the whole 70 bp? I was under the impression that SOPRA and like-minded assemblers relied on differential spacing between paired-end reads?
I think that the scenario here is that it is _my_ ignorance