Registry of Open Data on AWS

Usage examples for all datasets listed in the Registry of Open Data on AWS tagged with fastq.

The Singapore Nanopore Expression Data Set

Tutorials

Accessing the SG-NEx dataset on AWS by Ying Chen
Basecalling and analysing SG-NEx samples in S/BLOW5 format by Hasindu Gamaarachchi
Differential RNA modification analysis tutorial with xPore by Yu Song Chuah
Performing transcript discovery and quantification with Bambu by Min Hao Ling
RNA modification analysis tutorial with m6Anet by Yu Song Chuah

Tools & Applications

Bambu: Transcript discovery and quantification using long read RNA-Seq data by Ying Chen, Andre Sim et al.
JAFFAL: Detection of fusion genes from long read RNA-Seq data by Nadia M Davidson et al.
m6Anet: Identification of m6A from a single direct RNA-Seq sample by Christopher Hendra et al.
nf-core/nanoseq: A nanopore DNA and RNA-Seq demultiplexing, QC, alignment and analysis pipeline by Chelsea Sawyer et al.
xPore: Identification of differential RNA modification from direct RNA-Seq data by Ploy Pratanwanich et al.

Publications

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. by Ying Chen et al.
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. by Yuk Kei Wan et al.
Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. by Christopher Hendra et al.
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. by Ploy N Pratanwanich et al.
JAFFAL: Detecting fusion genes with long read transcriptome sequencing. by Nadia M Davidson et al.

PubSeq - Public Sequence Resource

Tutorials

Tools & Applications

Publications

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.

U.S. Environmental Protection Agency (EPA) Center for Computational Toxicology and Exposure High Throughput Transcriptomics Data

Tools & Applications

HTTr pipeline by Logan Everett

Publications

Benchmark Dose Modeling Approaches for Volatile Organic Chemicals Using a Novel Air-Liquid Interface In Vitro Exposure System by Speen A., Murray J., Krantz Q., Davies D., Evansky P., Harrill J., et al
Combining phenotypic profiling and targeted RNA-Seq reveals linkages between transcriptional perturbations and chemical effects on cell morphology: Retinoic acid as an example by Nyffeler J., Willis C., Harris F., Taylor L., Judson R., Everett L., et al
Exploring the Effects of Experimental Parameters and Data Modeling Approaches on In Vitro Transcriptomic Point-of-Departure Estimates by Harrill J., Everett L., Haggard D., Bundy J., Willis C., Shah I., et al
High-Throughput Transcriptomics of Water Extracts Detects Reductions in Biological Activity with Water Treatment Processes by Rogers J., Leusch F., Chambers B., Daniels K., Everett L., Judson R., et al
High-Throughput Transcriptomics Platform for Screening Environmental Chemicals by Harrill J., Everett L., Haggard D., Sheffield T., Bundy J., Willis C., et al
High-Throughput Transcriptomics Screen of ToxCast Chemicals in U-2 OS Cells by Bundy J., Everett L., Rogers J., Nyffeler J., Byrd G., Culbreth M., et al
Signature analysis of high-throughput transcriptomics screening data for mechanistic inference and chemical grouping by Harrill J., Everett L., Haggard D., Word L., Bundy J., Chambers B., et al

Caenorabditis Diversity Natural Resource

Tutorials

Data Releases - C. briggsae by Erik Andersen
Data Releases - C. elegans by Erik Andersen
Data Releases - C. tropicalis by Erik Andersen
FAQ - AWS API by Erik Andersen

Publications

CaeNDR, the Ceanorhabditis Natural Diversity Resource by Crombie TA, McKeown R, Moya ND, Evans KS, Widmayer SJ, LaGrassa V, et al.

NIH NCBI Sequence Read Archive (SRA) on AWS

Tutorials

Tools & Applications

SRA Toolkit by NCBI SRA

Publications

The Sequence Read Archive by Leinonen et al (2011)

1000 Genomes

Tutorials

Exploring Human Genetic Variation with 1000 Genomes in a Browser-Based Notebook on Scigantic by Scigantic

Tools & Applications

Examine genomic variation across populations with AWS by Konstantinos Tzouvanas

Publications

Exploratory data analysis of genomic datasets using ADAM and Mango with Apache Spark on Amazon EMR by Alyssa Marrow

The Human Microbiome Project

Publications

New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract by Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al
Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon

DNAStack COVID19 SRA Data

Tutorials

Viral lineage assignment by Heather Ward
AWS BatchAmazon EC2Amazon S3

Tools & Applications

Viral AI by DNAstack

Aging Mouse Brain Epigenetic

Publications

Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain by Zeng, Q., Wei, T., Klein, A., Bartlett, A., Liu, H., Nery, J.R., Castanon, R., Osteen, J., Johnson, N.D., Wang, W., Ding, W., Chen, H., Altshul, J., Kenworthy, M., Valadon, C., Owens, W., Wu, Z., Amaral, M.L., Song, Báez-Becerra, T.a.t.i.a.n.a., Cho, S., Chen, C., Willier, J., Cao, S., Rink, J., Lee, J., Barcoma, A., Arzavala, J., Emerson, N., Lu, Y.R., Ren, B., Behrens, M.a.r.g.a.r.i.t.a., Ecker, J.R.

COVID-19 Genome Sequence Dataset

Tools & Applications

Download SRA sequence data using Amazon Web Services (AWS) by NCBI SRA

Human PanGenomics Project

Publications

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes by Shafin et al (2020)

LongBench - cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

Tutorials

Benchmarking long-read DE gene and transcript analysis with edgeR by Yupei You

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

ONT Dataset Tutorials by EPI2MELabs

OpenWings OpenData

Tutorials

Tutorial I - UCE Phylogenomics by Brant Faircloth

Tools & Applications

phyluce by Brant Faircloth

Publications

Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales by BC Faircloth, JE McCormack, NG Crawford, MG Harvey, RT Brumfield, TC Glenn

1KG-ONT-VIENNA panel

Publications

Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project by Siegfried Schloissnig, Samarendra Pani, Bernardo Rodriguez-Martin, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Sarah Hunt, Tobias Rausch, Tobias Marschall, Jan O Korbel

Google Brain Genomics Sequencing Dataset for Benchmarking and Development

Publications

An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development by Baid G., Nattestad M., Kolesnikov A., Goel S., Yang H., Chang P., and Carroll A (2020)

If you want to add a dataset or usage example to this registry, please follow the instructions on the Registry of Open Data on AWS GitHub repository or tell us about your project.