Logan Unitigs and Contigs of the Sequence Read Archive (SRA) on AWS

Description

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 real 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 20-80x smaller size and higher quality genomic content.

Update Frequency

Occasional

License

NCBI Policy and NIH Genomic Data Sharing Policy

Documentation

https://github.com/IndexThePlanet/Logan

Managed By

Institut Pasteur (https://www.pasteur.fr)

See all datasets managed by Institut Pasteur (https://www.pasteur.fr).

Contact

rayan.chikhi@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.

Usage Examples

Tutorials

• Downloading unitigs of several accessions by Rayan Chikhi
  
• Downloading, mapping many contigs to a gene of interest by Rayan Chikhi
  
• Search for a k-mer of interest inside an unitigs accession by Rayan Chikhi
  

Tools & Applications

• Minia 3 by Rayan Chikhi
  
• Open Virome by Artem Babaian