HPG pore: an efficient and scalable framework for nanopore sequencing data

BMC Bioinformatics

Software

Joaquin Tarraga¹  Asunción Gallego¹  Joaquin Dopazo²  Vicente Arnau³  Ignacio Medina⁴ 

[1] Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain;Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain;Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain;Functional Genomics Node, (INB) at CIPF, 46012, Valencia, Spain;Departamento de Informática, ETSE, Universidad de Valencia, Valencia, Spain;HPC Service, University Information Services, University of Cambridge, Cambridge, UK;

关键词: File System;    FAST5 File;    FastQ File;    Hadoop Distribute File System;    Binary File;   

DOI  :  10.1186/s12859-016-0966-0

 received in 2015-09-03, accepted in 2016-02-22,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable.ResultsHere we present HPG Pore, a toolkit for exploring and analysing nanopore sequencing data. HPG Pore can run on both individual computers and in the Hadoop distributed computing framework, which allows easy scale-up to manage the large amounts of data expected to result from extensive use of nanopore technologies in the future.ConclusionsHPG Pore allows for virtually unlimited sequencing data scalability, thus guaranteeing its continued management in near future scenarios. HPG Pore is available in GitHub at http://github.com/opencb/hpg-pore.

【 授权许可】

CC BY   
© Tarraga et al. 2016