Hi all,
We have been running de novo assembly of a eukaryotic genome, using 454 titanium together with gsAssembler. When we compare our assembly with cloned cDNA fragments (sequenced with Sanger) we find some homopolymer errors. So we were wondering:
- Are there any reports on how common these errors are (especially in coding regions)?
- How have people dealt with these problems? We were thinking about running Illumina or SOLiD (which would give us 50-100x coverage) and use these data to correct the homopolymer run errors. Do you know of any programs or papers that might help?
thanks
/Jakub
We have been running de novo assembly of a eukaryotic genome, using 454 titanium together with gsAssembler. When we compare our assembly with cloned cDNA fragments (sequenced with Sanger) we find some homopolymer errors. So we were wondering:
- Are there any reports on how common these errors are (especially in coding regions)?
- How have people dealt with these problems? We were thinking about running Illumina or SOLiD (which would give us 50-100x coverage) and use these data to correct the homopolymer run errors. Do you know of any programs or papers that might help?
thanks
/Jakub
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