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Techniques & applications

A first genome assembly for nanopore sequencing

Nature Reviews Microbiology volume 13, page 459 (2015)Cite this article

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The 'MinION' nanopore sequencer works by applying an ionic current across an electrically resistant membrane permeabilized by protein nanopores. The sequence of DNA molecules passing through each nanopore is determined by measuring changes to this current. Nanopore sequencers can vastly increase the permissible length of input DNA and remove the need for DNA amplification; however, MinION has an error rate of ∼20% that calls for the development of error correction methods. Using DNA from Escherichia coli K-12 MG1655, Loman et al. now report the first genome assembly to be based solely on MinION data using a bioinformatics pipeline that reduced the error rate to ∼0.5%. First, errors were corrected using the consensus from iterative multiple alignments of overlapping sequence reads; next, the corrected reads were assembled into a genome; finally, the sequence was further corrected by comparison with raw electric current data from MinION using Nanopolish software. The resulting complete E. coli genome assembly is a milestone for nanopore sequencing.

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References

  1. Loman, N. J., Quick J. & Simpson J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods http://dx.doi.org/10.1038/nmeth.3444 (2015)

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  1. Naomi Attar
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Attar, N. A first genome assembly for nanopore sequencing. Nat Rev Microbiol 13, 459 (2015). https://doi.org/10.1038/nrmicro3548

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