Nanocall: an open source basecaller for Oxford Nanopore sequencing data.
The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls.



To allow offline and private analysis of MinION 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. Using R7.3 chemistry, 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 ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a MinION 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.



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



matei.david@oicr.on.caSupplementary information: Supplementary data are available at Bioinformatics online.
Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.
Matei
M
David
Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.
L J
LJ
Dursi
Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.
Delia
D
Yao
Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.|Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S 1A8, Canada.|Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada.
Paul C
PC
Boutros
Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.|Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada.
Jared T
JT
Simpson
D004247:DNA / Q000032:analysis*; D004926:Escherichia coli / Q000235:genetics; D006801:Humans; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004247:DNA