Nanocall: an open source basecaller for Oxford Nanopore sequencing data.
Bioinformatics
; 33(1): 49-55, 2017 01 01.
Article
em En
| MEDLINE
| ID: mdl-27614348
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 â¼68% identity, directly comparable to Metrichor '1D' data. Further, Nanocall is efficient, processing â¼2500 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. AVAILABILITY AND IMPLEMENTATION Nanocall is available at github.com/mateidavid/nanocall, released under the MIT license. CONTACT matei.david@oicr.on.caSupplementary information Supplementary data are available at Bioinformatics online.
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MEDLINE
Assunto principal:
Software
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DNA
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Análise de Sequência de DNA
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article