Cloud Indexes for Bowtie, Kraken, HISAT, and Centrifuge

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/jhu-indexes-dataset")

fs.listdir("s3://genome-idx")

Description:

Genomic tools use reference databases as indexes to operate quickly and efficiently, analogous to how web search engines use indexes for fast querying. Here, we aggregate genomic, pan-genomic and metagenomic indexes for analysis of sequencing data.

Contact:

Genomic tools use reference databases as indexes to operate quickly and efficiently, analogous to how web search engines use indexes for fast querying. Here, we aggregate genomic, pan-genomic and metagenomic indexes for analysis of sequencing data.

Update Frequency:

As new data becomes available; roughly quarterly

Managed By:

Langmead Lab at Johns Hopkins University & Kim Lab at University of Texas Southwestern

Resources:

1. resource:
   • Description: This bucket contains genomic indexes for Bowtie, Kraken, HISAT, and Centrifuge.
   • ARN: arn:aws:s3:::genome-idx
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, genomic, bioinformatics, biology, whole genome sequencing, medicine, reference index, mapping

Tutorials:

1. tutorial:
   • Title: Table of contents for tutorials for constituent tools
   • URL: https://benlangmead.github.io/aws-indexes/tutorial
   • AuthorName: Ben Langmead
   • AuthorURL: https://benlangmead.github.io/aws-indexes

Publication:

1. publication:
   • Title: Reducing reference bias using multiple population reference genomes
   • URL: https://www.biorxiv.org/content/10.1101/2020.03.03.975219v4.full.pdf
   • AuthorName: Chen et al (2020)