Presented at London Calling 2016

Included in nanopore theme

Altmetric score 70.61 (top 1.5%)

Author: Matei David
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Research area: bioinformatics
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Open peer-review

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Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data


Created on 28th March 2016

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


Motivation: 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. Results: 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. On two ecoli 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 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. Availability: Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license. Contact: matei.david at oicr.on.ca

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