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bioRxiv · 10.1101/046086

Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data

Matei David·Lewis Jonathan Dursi·Delia Yao·Paul C Boutros·Jared T Simpson
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Abstract

MotivationThe highly portable Oxford Nanopore MinlON sequencer has enabled new applications of genome sequencing directly in the field. However, the MinlON currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.\n\nResultsTo allow offline and private analysis of MinlON data, we created Nanocall. Nanocall is the first freely-available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. On two E.coli and two human samples, with natural as well as PCR-amplified DNA, Nanocall reads have ~68% identity, directly comparable to Metrichor \"1D\" data. Further, Nanocall is efficient, processing ~500Kbp of sequence per core hour, and fully parallelized. Using 8 cores, Nanocall could basecall a MinlON sequencing run in real time. Metrichor provides the ability to integrate the \"1D\" sequencing of template and complement strands of a single DNA molecule, and create a \"2D\" read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data.\n\nAvailabilityNanocall is available at github.com/mateidavid/nanocall, released under the MIT license.\n\nContactmatei.david at oicr.on.ca

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Matei David, Lewis Jonathan Dursi, Delia Yao, Paul C Boutros, Jared T Simpson. 2016-03-28. Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data. https://doi.org/10.1101/046086

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