I de novo assembled a novel bacterial genome to contigs and would like to close the gabs between these contigs using an in silico method.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515008/ This seems like a promising method though it was designed for eukaryotic genomes. Moreover some of the older methods reviewed in the paper might be helpful too.
Plus if you have the resources, the best way to go would be PacBio http://www.pacb.com/
You can use scaffolding tools to organise contigs. But ultimately if your library insert size is smaller than the repetitive sequence in your genome, then you will not be able to fully close it. It will depend on the sequencing method you used to start with
Thanks Andrew, I'm using Miseq paired-end reads (~300bp ), usually I use Mauve Contig Mover (MCM) to order a draft genome when the reference available.
With illumina unless you have a mate pair library as well as a paired end Library. It is unlikely that yiu will be able to close the genome in silco , as the paired end reads will not have big enough inserts to cover the repaets
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