Dataset Information

Streamlining remote nanopore data access with slow5curl.

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.

SUBMITTER: Wong B

PROVIDER: S-EPMC11010652 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Publications

Streamlining remote nanopore data access with slow5curl.

Wong Bonson B Ferguson James M JM Do Jessica Y JY Gamaarachchi Hasindu H Deveson Ira W IW

GigaScience 20240101

<h4>Background</h4>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.<h4>Results</h4>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 rep ...[more]

PMID: 38608279

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Dataset Information

Streamlining remote nanopore data access with slow5curl.

Background

Results

Conclusions

Publications

Streamlining remote nanopore data access with slow5curl.

Similar Datasets

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