Hi, has anyone assembled just a plasmid with Illumina data? What is the best way? My go-to way for assembly has been VelvetOptimiser (for like everything), but it is estimating a very small coverage compared to what it should be in this case, and so it is giving a very large discontiguous assembly.
Extra info: Data are from a MiSeq, a 2x150bp PE run, with the following read metrics. The expected size is 160kb (646x unfiltered coverage).
avgReadLength totalBases maxReadLength minReadLength avgQuality numReads 142.60 103482648 151 35 34.85 725682
Fastqc reports 62% duplication levels unfortunately, but it still leaves a large coverage.