We sequenced a Pseudomonas genome which resulted in several 454 scaffolds. From examining the sequence data it looks like there are many gaps in the sequence because of repeated rRNA genes. Newbler appears to have left these regions as gaps in the sequence because the repeats cannot be resolved.
We are considering using Illumina sequencing to close these gaps, however we are not sure if this will solve the problem either. If we use mate-pair Illumina will this help to bridge these repeated regions? Otherwise what other options do we have as there are many of these repeats and manual PCR is turning out to be laborious and expensive.
We are considering using Illumina sequencing to close these gaps, however we are not sure if this will solve the problem either. If we use mate-pair Illumina will this help to bridge these repeated regions? Otherwise what other options do we have as there are many of these repeats and manual PCR is turning out to be laborious and expensive.
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