Poretools: a toolkit for analyzing nanopore sequence data

By Nicholas J. Loman, Aaron R. Quinlan. bioRxiv, 2014

414 citations recorded by the source corpus.

Motivation Nanopore sequencing may be the next disruptive technology in genomics. Nanopore sequencing has many attractive properties including the ability to detect single DNA molecules without prior amplification, the lack of reliance on expensive optical components, and the ability to sequence very long fragments. The MinION from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialised and is now available to early-access users. The MinION™ is a USB-connected, portable nanopore sequencer which permits real-time analysis of streaming event data. A cloud-based service is available to translate events into nucleotide base calls. However, software support to deal with such data is limited, and the community lacks a standardized toolkit for the analysis of nanopore datasets. Results We introduce poretools, a flexible toolkit for manipulating and exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (a variant of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. Availability and implementation Poretools is open source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code and user documentation are freely available in Github at https://github.com/arq5x/poretools Supplementary information An IPython notebook demonstrating the use and functionality of poretools in greater detail is available from the Github repository.

Subfields: Biomedical Engineering, Molecular Biology, Structural Biology

View Paper: https://www.semanticscholar.org/paper/855d8da9a8f8972228e637c998b44d89c80728b6

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Citations in the corpus

A complete bacterial genome assembled de novo using only nanopore sequencing data (2015, methodology): “The FASTA sequences for reads were extracted using poretools 10 .”
PLSDB: a resource of complete bacterial plasmids (2018, methodology): “The reads were extracted to FASTA files using Poretools (26) (version 0.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, background): “01492) and poretools for long read sequencing analysis (19); MultiQC (20) to aggregate multiple results into a single report; a new RNA-seq analysis tool suite with modern analysis tools such as Kallisto (21), Salmon (22), Deseq2 (23) and STAR-Fusion (24), and GenomeSpace (25), a cloud-based interop”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “The FASTA sequences for reads are extracted using Poretools [21] and converted to the format expected by alignment tool DALIGNER [37].”
The sequence of sequencers: The history of sequencing DNA (2016, background): “3b) [89,90], the latter of which is a small, mobile phone sized USB device, which was ﬁ rst released to end users in an early access trial in 2014 [91].”
Real-time, portable genome sequencing for Ebola surveillance (2016, background): “30MRIGlobal, Kansas City, Missouri 64110-2241, USA.”
NanoPack: visualizing and processing long-read sequencing data (2018, methodology): “Earlier tools such as poretools (Loman and Quinlan, 2014), poRe (Watson et al. , 2015) and IONiseR (Smith, 2017) mainly focused on feature extraction from the older fast5 file formats, and alternative tools such as pycoQC (Leger, 2017) and minion_qc (Lanfear, n.d. https://…”
Detecting DNA cytosine methylation using nanopore sequencing (2017, methodology): “First we extract the “two-direction” (2D) reads from a MinION run using poretools [3].”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “We used the two-dimensional reads available for download from the PBcR wiki page, which were already converted to FASTQ format using poretools [21].”