PyPore: a python toolbox for nanopore sequencing data handling

• DOI: 10.1093/bioinformatics/btz269
• Publication Date: 2019-04-10T11:14:22Z
• Authors: Roberto Semeraro; Alberto Magi
• Keywords: 0301 basic medicine; Nanopore Sequencing; Nanopores; 03 medical and health sciences; Genome; High-Throughput Nucleotide Sequencing; nanopore sequencing data quality; Sequence Analysis, DNA; Software

Abstract

Motivation The recent technological improvement of Oxford Nanopore sequencing pushed the throughput of these devices to 10–20 Gb allowing the generation of millions of reads. For these reasons, the availability of fast software packages for evaluating experimental quality by generating highly informative and interactive summary plots is of fundamental importance.

Results We developed PyPore, a three module python toolbox designed to handle raw FAST5 files from quality checking to alignment to a reference genome and to explore their features through the generation of browsable HTML files. The first module provides an interface to explore and evaluate the information contained in FAST5 and summarize them into informative quality measures. The second module converts raw data in FASTQ format, while the third module allows to easily use three state-of-the-art aligners and collects mapping statistics.

Availability and implementation PyPore is an open-source software and is written in Python2.7, source code is freely available, for all OS platforms, in Github at https://github.com/rsemeraro/PyPore

Supplementary information Supplementary data are available at Bioinformatics online.