Hi, I'm very much new to the field of metagenomics and sequencing. I have been trying to find out answers for this but I haven't been too successful probably because the answer is too obvious or my understanding is completely plainly wrong... Anyway, it would be great if some of you could enlighten me with an answer!
In metagenomics, say a soil sample is taken for sequencing. Now, fragmented genomes from this mixture of species are sequenced say by 454 sequencing. My question is, will there always be some overlapping regions to guide de novo assembly? If I am understanding this correctly (probably not!), there will be abundant species in the sample and their genomes will be fairly easy to assemble as there are lots of them, but for the less abundant species, there won't be enough of them to have enough overlapping regions of the genomes for de novo assembly. I know this is a bit extreme, but what if there happens to be just one member of a novel species in the sample? is there just no way for the whole genome of this species to be sequenced?
In metagenomics, say a soil sample is taken for sequencing. Now, fragmented genomes from this mixture of species are sequenced say by 454 sequencing. My question is, will there always be some overlapping regions to guide de novo assembly? If I am understanding this correctly (probably not!), there will be abundant species in the sample and their genomes will be fairly easy to assemble as there are lots of them, but for the less abundant species, there won't be enough of them to have enough overlapping regions of the genomes for de novo assembly. I know this is a bit extreme, but what if there happens to be just one member of a novel species in the sample? is there just no way for the whole genome of this species to be sequenced?
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