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Old 11-03-2017, 04:39 AM   #8
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Location: Bioinformatics Institute, SPb

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Originally Posted by JonB View Post

I am trying to assemble a eukaryotic genome of about 300MB. I have Illumina data, and I am thinking of trying out the MinION Basic Starter Pack to use for scaffolding. But it produces only 1D reads, can it still be used for scaffolding in combination with Illumina data?


If you got plenty of computational resources, run several assemblies and then see which one does best. If you are moderately successful with your 1D runs, you'll generate about 10 Gb of data from two flow cells, which is 30x - just about borderline for which assembler to choose. Should you have really high coverage of long reads, classical long-read assemblers like canu or miniasm+racon combo would give you best results. After that you'd run nanopolish, and then pilon with your Illumina data, and would probably have 99.(2..8)% correct assembly.

If you end up with less nanopore (10-20X) but lots (100Х+) of Illumina, do give Masurca a shot, it should perform best.
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