Skip to content
Open
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 29 additions & 0 deletions datasets/krepp-idx.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
Name: Reference Indexes for krepp
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.
Documentation: https://github.com/bo1929/krepp/wiki/Available-reference-indexes
Contact: https://github.com/bo1929/krepp/issues
ManagedBy: Mirarab Lab at UC San Diego
UpdateFrequency: Quarterly or as new data becomes available
Tags:
- bioinformatics
- metagenomics
- microbiome
- reference index
- phylogenetics
- life sciences
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.
Resources:
- 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.
ARN: arn:aws:s3:::krepp-idx
Region: us-west-1
Type: S3 Bucket
DataAtWork:
Tutorials:
- Title: Tutorial for using krepp indexes for metagenomic sequence analysis.
URL: https://github.com/bo1929/krepp/wiki/Tutorial
AuthorName: Ali Osman Berk Sapci
AuthorURL: https://bo1929.github.io/
Publications:
- Title: A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.
URL: https://www.biorxiv.org/content/10.1101/2025.01.20.633730v2
AuthorName: Sapci et al. (2024)