We're assembling de novo bacterial genomes with ILMN system. After the first run, we have N50 about 120-150 kb and are now trying different assemblers to orient configs relative to each other and align them to related genomes. A question arose during this process: how can I define the point where I should stop with in-silico and move to the next NGS run or fill the gaps with Sanger?
N50 of 120 kb is good for baterial genome assembly. For your question, IMHO the ultimate answer is "it's up to you". It is important you describe what you did, what parameters you used, and whether you did some cross check by wet-experiment or reference sequences. For in-depth discussions, here are some publications:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031002
http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024182
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