Oxford Nanopore Technologies Open Datasets

ONT Open Datasets Tutorials

September 22, 2020

Below you will find helpful information and links out to tutorials for datasets within the Open Datasets project.

How can I access the data?

All the data is stored under in an Amazon Web Services S3 bucket:

s3://ont-open-data

This public has public permissions for anyone to obtain the data without requiring login credentials. To download the data we recommend using the AWS command line interface. With the CLI installed listing the datasets can be performed with:

aws s3 ls --no-sign-request s3://ont-open-data/

There will be a subdirectory per dataset release. Inside each dataset will be contained a README.md file with brief details. This website will contain additional details for each dataset.

To download datasets or extracts thereof we recommend using the sync command:

aws s3 sync --no-sign-request s3://ont-open-data/gm24385_2020.09 gm24385_2020.09

Datasets may be added to or amended over time so using sync can be used with a previously fetch copy to update with the latest changes and additions.

Running workflows using ONT’s EPI2ME platform

Oxford Nanopore’s EPI2ME platform includes several workflows for analysing genomics datasets in the cloud with Amazon Web Services, reducing the computational burden on the users local compute infrastructure. For example, the FASTQ Human Alignment GRCh38 can be used to perform alignment of nanopore sequencing reads to the human reference genome to obtain industry standard BAM file outputs.

How can I recreate the analysis directories?

With each dataset release we will include details of how the analysis directories were constructed from the primary inputs. For example for the GM24385 dataset release this page contains details of the Snakemake pipeline used.


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