ArticleBMC bioinformatics2016
HPG pore: an efficient and scalable framework for nanopore sequencing data.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- Sequoia: A Framework for Visual Analysis of RNA Modifications from Direct RNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets.BMC genomics · 2021Article
- Article
- A new parallel pipeline for DNA methylation analysis of long reads datasets.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.