Streamlining Remote Nanopore Data Access with Slow5curl

Overview

Journal Gigascience

Publisher Oxford University Press

Specialties Biology
Genetics

Date 2024 Apr 12

PMID 38608279

Authors

Bonson Wong

James M Ferguson

Jessica Y Do

Hasindu Gamaarachchi

Ira W Deveson

Affiliations

Soon will be listed here.

Abstract

Background: As adoption of nanopore sequencing technology continues to advance, the need to maintain large volumes of raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl, a software package designed to streamline nanopore data sharing, accessibility, and reanalysis.

Results: Slow5curl allows a user to fetch a specified read or group of reads from a raw nanopore dataset stored on a remote server, such as a public data repository, without downloading the entire file. Slow5curl uses an index to quickly fetch specific reads from a large dataset in SLOW5/BLOW5 format and highly parallelized data access requests to maximize download speeds. Using all public nanopore data from the Human Pangenome Reference Consortium (>22 TB), we demonstrate how slow5curl can be used to quickly fetch and reanalyze raw signal reads corresponding to a set of target genes from each individual in large cohort dataset (n = 91), minimizing the time, egress costs, and local storage requirements for their reanalysis.

Conclusions: We provide slow5curl as a free, open-source package that will reduce frictions in data sharing for the nanopore community: https://github.com/BonsonW/slow5curl.

Citing Articles

Streamlining remote nanopore data access with slow5curl.

Wong B, Ferguson J, Do J, Gamaarachchi H, Deveson I Gigascience. 2024; 13.

PMID: 38608279 PMC: 11010652. DOI: 10.1093/gigascience/giae016.

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