Description

krepp is an alignment-free method for estimating distances and phylogenetic placement of individual reads to many thousands of reference genomes in a scalable manner using k-mers. This dataset includes k-mer-based indexes consisting of ultra-large reference genome sets that can be efficiently analyzed using krepp.

Update Frequency

Quarterly or as new data becomes available

License

GPL-3.0 license. Use of the data should be cited in the usual way, following https://github.com/bo1929/krepp/tree/master?tab=readme-ov-file#citation.

Documentation

https://github.com/bo1929/krepp/wiki/Available-reference-indexes

Managed By

Mirarab Lab at UC San Diego

See all datasets managed by Mirarab Lab at UC San Diego.

Contact

https://github.com/bo1929/krepp/issues

How to Cite

Reference Indexes for krepp was accessed on DATE from https://registry.opendata.aws/kreppref.

Usage Examples

Tutorials

Tutorial for using krepp indexes for metagenomic sequence analysis. by Ali Osman Berk Sapci

Publications

A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement. by Sapci et al. (2024)

Resources on AWS

Description

This dataset contains genomic indexes for various reference datasets in binary format. Using krepp, you can perform distance estimation and phylogenetic placement with respect to these indexes.

Resource type

S3 Bucket

Amazon Resource Name (ARN)

arn:aws:s3:::kreppref

AWS Region

us-west-1

AWS CLI Access (No AWS account required)

aws s3 ls --no-sign-request s3://kreppref/