David Eccles, who provides excellent update on the latest advances related to Oxford Nanopore technology, pointed out that two new open source base-callers have been released last week. So far the researchers relied on the proprietary software provided by Oxford Nanopore, and that required having internet connection in remote locations. It is also noteworthy that at least the second paper claims to improve basecalling accuracy (“By employing carefully crafted recurrent neural networks, our tool improves the base calling accuracy compared to the default base caller supplied by the manufacturer.”). Overall, these are very exciting times in the sequencing world.
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
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that the error rate can be reduced by improving the base calling process.
Results: We present the first open-source DNA base caller for the MinION sequencing platform by Oxford Nanopore. By employing carefully crafted recurrent neural networks, our tool improves the base calling accuracy compared to the default base caller supplied by the manufacturer. This advance may further enhance applicability of MinION for genome sequencing and various clinical applications.
Availability: DeepNano can be downloaded at this http URL