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Old 03-08-2017, 05:07 AM   #11
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Originally Posted by SDPA_Pet View Post
They are soil samples. I did shotgun metagenomics and I am insterested in microbial communities. I will not assemble it, because normally less than 1% of reads can be assemble. My plan is joined whatever reads can be joined and get longer reads. Then, to annotate it using the long reads. Those samples are from environments and you don't really have prior knowledge about what is in it. The workflow is different from model organism.
SPAdes has a meta option for doing assemblies with metagenomes. I am sure there are other options for this type of assemblies. You would need access to a server with ample RAM but it should be possible to assemble the data you have to some extent. Unless you have already tried this and are reporting 1% assembly based on that.

PS, I don't understand in your previous post about "If you have a reference available then making the libraries so the two ends do not overlap makes sense since you can sample a larger region". Just curious.
As long as you can map the two ends of a fragment on a reference genome at the expected distance you could consider that region as "sampled". Since you will have reads that will randomly cover the genome, you should get reads mapping/spanning across entire genome.
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