Open data
|
Deployed on AWS
This repository is a re-analysis of the NCBI Sequence Read Archive (SRA), December 2023 freeze, to make it more accessible. The SRA is an open access database of biological sequences, containing raw data from high-throughput DNA and RNA sequencing platforms. It is the largest database of public DNA sequences worldwide, containing a wealth of genomic diversity across all living organisms. This repository contains Logan, a set of compressed FASTA files for all individual SRA accessions, in the form of unitigs and contigs. Borrowing methods from the realm of genome assembly, unitigs preserve nearly all the information present in the original sample, whereas contigs get rid of variations to increase sequence lengths. Altogether, Logan recapitulates the information present in the SRA while making it an order of magnitude more accessible due to 20-100x smaller size and higher quality genomic content.
Overview
This repository is a re-analysis of the NCBI Sequence Read Archive (SRA), December 2023 freeze, to make it more accessible. The SRA is an open access database of biological sequences, containing raw data from high-throughput DNA and RNA sequencing platforms. It is the largest database of public DNA sequences worldwide, containing a wealth of genomic diversity across all living organisms. This repository contains Logan, a set of compressed FASTA files for all individual SRA accessions, in the form of unitigs and contigs. Borrowing methods from the realm of genome assembly, unitigs preserve nearly all the information present in the original sample, whereas contigs get rid of variations to increase sequence lengths. Altogether, Logan recapitulates the information present in the SRA while making it an order of magnitude more accessible due to 20-100x smaller size and higher quality genomic content.
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
Vendors are responsible for their product descriptions and other product content. AWS does not warrant that vendors' product descriptions or other product content are accurate, complete, reliable, current, or error-free.
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
- Compressed FASTA files (.fa.zst) in a public S3 bucket: all unitigs and contigs of SRA accessions.
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::logan-pub
- AWS region
- us-east-1
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://logan-pub/
Resources
Vendor resources
Support
Contact
Managed By
Institut Pasteur (https://www.pasteur.fr )
How to cite
Logan Unitigs and Contigs of the Sequence Read Archive (SRA) on AWS was accessed on DATE from https://registry.opendata.aws/pasteur-logan .
License
Similar products
This complimentary sample of hourly Historical Weather data is for 50 U.S. Capital cities and represents a small snippet of the massive Weather Source historical global weather archive that goes back to the year 2000 (available in both hourly & daily resolution). With its 21 supported weather parameters, the Weather Source OnPoint historical database is the most comprehensive database in the industry that was designed and developed for analytics and machine learning.