Refgenie reference genome assets

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://awspds.refgenie.databio.org")

Description:

Pre-built refgenie reference genome data assets used for aligning and analyzing DNA sequence data.

Contact:

Pre-built refgenie reference genome data assets used for aligning and analyzing DNA sequence data.

Update Frequency:

As new data becomes available (roughly quarterly)

Managed By:

Sheffield lab at the University of Virginia

Resources:

1. resource:
   • Description: Refgenie S3 Bucket
   • ARN: arn:aws:s3:::awspds.refgenie.databio.org
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, biology, bioinformatics, genetic, genomic, infrastructure, life sciences, single-cell transcriptomics, transcriptomics, whole genome sequencing

Tutorials:

1. tutorial:
   • Title: Basic Refgenie tutorial
   • URL: http://refgenie.databio.org/en/latest/tutorial/
   • AuthorName: Nathan Sheffield
   • AuthorURL: http://www.databio.org
   • Services: None

Tools & Applications:

1. tools & applications:

   • Title: Pipeline for ATAC-seq data analysis
   • URL: http://pepatac.databio.org
   • AuthorName: Jason Smith and Nathan Sheffield
   • AuthorURL: http://databio.org

2. tools & applications:

   • Title: Pipeline for PRO-seq data analysis
   • URL: http://peppro.databio.org
   • AuthorName: Jason Smith and Nathan Sheffield
   • AuthorURL: http://databio.org

Publication:

1. publication:
   • Title: Refgenie: a reference genome resource manager
   • URL: https://doi.org/10.1093/gigascience/giz149
   • AuthorName: Michał Stolarczyk, Vincent P Reuter, Jason P Smith, Neal E Magee, Nathan C Sheffield
   • AuthorURL: http://www.databio.org