MetaGraph Sequence Indexes

Description

The MetaGraph Sequence Indexes dataset comprises full-text searchable index files for raw sequencing data hosted in major public repositories. These include the European Nucleotide Archive (ENA) managed by the European Bioinformatics Institute (EMBL-EBI), the Sequence Read Archive (SRA) maintained by the National Center for Biotechnology Information (NCBI), and the DNA Data Bank of Japan (DDBJ) Sequence Read Archive (DRA).All index files can be used with the MetaGraph framework for sequence search. Indexes can be jointly used for aggregated search in the cloud or can be individually downloaded for search using local hardware.

Update Frequency

Continuously as new sequencing data becomes available.

License

CC BY-SA 4.0

Documentation

Documentation of the dataset available under https://github.com/ratschlab/metagraph-open-data Documentation of the MetaGraph framework is available under https://metagraph.ethz.ch/

Managed By

Biomedical Informatics Lab, ETH Zurich, Switzerland

See all datasets managed by Biomedical Informatics Lab, ETH Zurich, Switzerland.

Contact

Please open an issue under https://github.com/ratschlab/metagraph-open-data/issues

How to Cite

MetaGraph Sequence Indexes was accessed on DATE from https://registry.opendata.aws/metagraph. Karasikov M, Mustafa H, Danciu D, Zimmermann M, Barber C, Raetsch G, Kahles A. Indexing All Life’s Known Biological Sequences. Preprint (2024). doi: 10.1101/2020.10.01.322164

Usage Examples

Tutorials

• Usage within AWS by Oleksandr Kulkov
  AWS CloudFormationAWS Step FunctionsAWS LambdaAWS BatchAmazon S3Amazon SNS

Tools & Applications

• CloudFormation stack with a Step Function for dataset queries via AWS Batch by Oleksandr Kulkov
  

Publications

• A global metagenomic map of urban microbiomes and antimicrobial resistance by Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KE, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, et al.