Hi there,
I'm working on an eukaryot and we have Illumina and 454 data.
After many hybrid assembly approaches a "simple" Allpaths-LG assembly of the Illumina data yielded the best results.
I also tried (hybrid) approaches with Newbler, CLC bio's assembly cell, SOAPdenovo and MIRA.
After the finished Allpaths-LG assembly I used a script that mapped the 454 data on the scaffolds and looked for overlaps on either end of a gap (a stretch of Ns). This gap was closed or shortened, whenever possible.
The results were better, but only very marginal.
Any other ideas how I could improve the result and find a good way of incorporating the 454 data?
Thanks
I'm working on an eukaryot and we have Illumina and 454 data.
After many hybrid assembly approaches a "simple" Allpaths-LG assembly of the Illumina data yielded the best results.
I also tried (hybrid) approaches with Newbler, CLC bio's assembly cell, SOAPdenovo and MIRA.
After the finished Allpaths-LG assembly I used a script that mapped the 454 data on the scaffolds and looked for overlaps on either end of a gap (a stretch of Ns). This gap was closed or shortened, whenever possible.
The results were better, but only very marginal.
Any other ideas how I could improve the result and find a good way of incorporating the 454 data?
Thanks

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