Hi all,
I am currently trying to assemble a 5mb bacterial genome. I have 43bp single end reads from an Illumina Genome Analyzer IIx and 500bp double end reads from a Roche 454 GS FLX and was wondering if anyone had any luck with hybrid de novo assembly for these library types. I have read that putting the illumina data into velvet, using EMBOSS to cut the resulting contigs down a bit, and then combining it with the 454 data in Newbler gets decent results but that was two years ago so I didn't know if there was a higher quality pipeline to go with now.
Thanks
I am currently trying to assemble a 5mb bacterial genome. I have 43bp single end reads from an Illumina Genome Analyzer IIx and 500bp double end reads from a Roche 454 GS FLX and was wondering if anyone had any luck with hybrid de novo assembly for these library types. I have read that putting the illumina data into velvet, using EMBOSS to cut the resulting contigs down a bit, and then combining it with the 454 data in Newbler gets decent results but that was two years ago so I didn't know if there was a higher quality pipeline to go with now.
Thanks
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