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Streamlining remote nanopore data access with slow5curl.

Bonson Wong1,2,3, James M Ferguson1,2, Jessica Y Do1,2,3

  • 1Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.

Gigascience
|April 12, 2024
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Summary
This summary is machine-generated.

Nanopore sequencing generates large raw signal data. The new slow5curl tool enables efficient, targeted data retrieval and reanalysis from remote servers, reducing storage and costs.

Keywords:
cloudnanoporeraw signalsequencing datasignal data

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Nanopore sequencing generates vast amounts of raw current signal data.
  • Reanalyzing this data with updated algorithms presents storage and accessibility challenges.
  • Efficient data sharing and access are crucial for the growing nanopore community.

Purpose of the Study:

  • Introduce slow5curl, a software package to streamline nanopore data sharing, accessibility, and reanalysis.
  • Enable users to fetch specific reads from large remote nanopore datasets without downloading entire files.

Main Methods:

  • slow5curl utilizes an index for rapid read fetching from SLOW5/BLOW5 formatted data.
  • Employs highly parallelized data access requests to optimize download speeds.
  • Demonstrated on >22 TB of Human Pangenome Reference Consortium nanopore data.

Main Results:

  • slow5curl successfully fetched and reanalyzed raw signal reads for target genes from a large cohort (>22 TB).
  • Significantly minimized time, egress costs, and local storage requirements for reanalysis.
  • Showcased efficient data retrieval from large-scale nanopore datasets.

Conclusions:

  • slow5curl is a free, open-source package designed to reduce data sharing friction in the nanopore community.
  • Facilitates efficient reanalysis of large nanopore datasets.
  • Provides a solution for managing and accessing large volumes of raw nanopore signal data.