We are starting a number of large (1.5-4 Gb) fish de novo genome sequencing projects. The AllPaths-LG assembler seems to be producing the best genomes of these types. I am wondering what is the best stategy for overlapping PE libraries for an AllPaths assembly. We were going to sequence 6 lanes of Hi-Seq rapid mode, to get around 100x coverage. Is it best to make one PE library and spread it over the 6 lanes, one library for each lane, or something in between?
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