Assembly

[P-Richmond]

Hello SEQanswers,
We're going to be de novo assembling a genome of an organism with a genome size between 20-50MB. We're looking for recommendations on what types (454, Illumina SIPES, Illumina LIPES, or others) and any combinations of sequencing platforms/libraries are currently producing the best results for de novo assembly.

We are also looking for a recommended minimum read depth/count for producing a high quality draft genome.

If this is talked about in a separate thread please direct me to it.

Thanks,
Phil

[krobison]

You might start by looking at Lex Nederbragt's recent blog post on sequencing bacterial genomes; it's a reasonable guide though you are clearly going for much larger quarry. I just noticed he doesn't cover read depth, but for a lot of projects 100X is a good place to start.

My personal bent for this sort of project would be to start with 100X or more 2x100 coverage on the Illumina HiSeq. That will get you a rough draft. Mate pair libraries or Pac Bio reads are the current favorites for getting those into large scaffolds. For PacBio, you may not need such high coverage, but I don't know a good rule-of-thumb there; Michael Schatz has published on this & also has some of his slide decks on line.

454 is fading as a WGS platform; very expensive for what it gets you. Ion Torrent/Proton really hasn't caught on.

You might also look into OpGen optical mapping for scaffolding, though that may not come cheaply. There are other companies which may have solutions in this space in the near future (e.g. BioNano Genomics, Oxford Nanopore), but who knows when they will actually be available.