2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2016
Abstrakt

Matei David, L. J. Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson. Nanocall: An Open Source Basecaller for Oxford Nanopore Sequencing Data. Bioinformatics, 2016.

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Abstract:

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. 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 ~2500Kbp 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. AVAILABILITY:
Nanocall is available at github.com/mateidavid/nanocall, released under the MIT
license. CONTACT: matei.david at oicr.on.ca SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics.