Nanocall: an open source basecaller for Oxford Nanopore sequencing data.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The Oxford Nanopore MinION sequencer facilitates field-based genome sequencing.
• Current MinION data analysis relies on the cloud-based Metrichor platform for basecalling.
• There is a need for offline and private analysis solutions for MinION data.

Purpose of the Study:

• To develop an open-source, offline basecaller for Oxford Nanopore MinION sequencing data.
• To provide a freely available alternative to cloud-based basecalling solutions.
• To enable private and efficient analysis of MinION sequencing data.

Main Methods:

• Development of Nanocall, a novel open-source basecaller.
• Testing Nanocall on E.coli and human samples using R7.3 chemistry.
• Evaluation of Nanocall's read identity, efficiency, and processing speed.

Main Results:

• Nanocall achieves approximately 68% read identity, comparable to Metrichor's 1D data.
• The basecaller processes approximately 2500 Kbp per core hour, demonstrating high efficiency.
• Real-time basecalling of a MinION run was achieved on a 4-core desktop computer.

Conclusions:

• Nanocall is the first freely available, open-source, offline basecaller for Oxford Nanopore sequencing.
• The software enables private and efficient analysis of MinION data.
• Future development will focus on integrating 2D read capabilities.