Open data
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Deployed on AWS
The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Examples include: NA12878 (HG001) and NA24385 (HG002) sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 flowcells; and, UHR RNA (direct-RNA) on an ONT PromethION using the latest RNA004 flowcells. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format, and can be rebasecalled when basecalling software updates bring accuracy and feature improvements over the years. Raw signal data is not only for rebasecalling, but also can be used for emerging bioinformatics tools that directly analyse raw signal data. We also provide the basecalled data alongside the raw signal data.
Overview
The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Examples include: NA12878 (HG001) and NA24385 (HG002) sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 flowcells; and, UHR RNA (direct-RNA) on an ONT PromethION using the latest RNA004 flowcells. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format, and can be rebasecalled when basecalling software updates bring accuracy and feature improvements over the years. Raw signal data is not only for rebasecalling, but also can be used for emerging bioinformatics tools that directly analyse raw signal data. We also provide the basecalled data alongside the raw signal data.
Features and programs
Open Data Sponsorship Program
This dataset is part of the Open Data Sponsorship Program, an AWS program that covers the cost of storage for publicly available high-value cloud-optimized datasets.
Pricing
This is a publicly available data set. No subscription is required.
Legal
Content disclaimer
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Delivery details
AWS Data Exchange (ADX)
AWS Data Exchange is a service that helps AWS easily share and manage data entitlements from other organizations at scale.
Open data resources
Available with or without an AWS account.
- How to use
- To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more
- Description
- Currently, the dataset contains two reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format. Basecalls are available in bgzip compressed FASTQ format. Alignments are available in BAM format. More information can be found at https://github.com/GenTechGp/gtgseq/blob/main/docs/data.md.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::gtgseq
- AWS region
- us-west-2
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://gtgseq/
Resources
Vendor resources
Support
Contact
Managed By
Genomic Technologies Group, Garvan Institute of Medical Research (https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab )
How to cite
Garvan Institute Long Read Sequencing Benchmark Data was accessed on DATE from https://registry.opendata.aws/gtgseq .