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


Type

Article

Change log

Authors

Tarraga, Joaquin 
Gallego, Asunción 
Arnau, Vicente 
Medina, Ignacio 
Dopazo, Joaquin 

Abstract

BACKGROUND: The 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. RESULTS: Here 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. CONCLUSIONS: HPG 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.

Description

Keywords

DNA, Nanopores, Sequence Analysis, DNA

Journal Title

BMC Bioinformatics

Conference Name

Journal ISSN

1471-2105
1471-2105

Volume Title

Publisher

Springer Science and Business Media LLC