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Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data

Matei David, L.J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson
doi: https://doi.org/10.1101/046086
Matei David
1Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
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L.J. Dursi
1Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
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Delia Yao
1Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
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Paul C. Boutros
1Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
2Department of Pharmacology and Toxicology, University of Toronto, Toronto, M5S 1A8, Canada
3Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
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Jared T. Simpson
1Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
4Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
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ABSTRACT

Motivation The 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.

Results To 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.

Availability Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license.

Contact matei.david at oicr.on.ca

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 28, 2016.
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Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data
Matei David, L.J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson
bioRxiv 046086; doi: https://doi.org/10.1101/046086
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Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data
Matei David, L.J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson
bioRxiv 046086; doi: https://doi.org/10.1101/046086

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