Registry of Open Data on AWS

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

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5, 3.7, 4.0, 4.2, and 4.4

Tutorials

Tools & Applications

Publications

Accurate and efficient calling of small and large variants from popgen datasets using the DRAGEN Bio-IT Platform by Illumina Inc. (2021)
Data solution empowering population genomics by Illumina Inc. (2021)
Demystifying the versions of GRCh38/hg38 reference genomes, how they are used in DRAGEN and their impact on accuracy by Illumina Inc. (2021)
DRAGEN Sets New Standard for Data Accuracy in PrecisionFDA Benchmark Data. Optimizing Variant Calling Performance with Illumina Machine Learning and DRAGEN Graph by Illumina Inc. (2022)
DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2020)
Genotyping variants at population scale using DRAGEN gVCF Genotyper by Illumina Inc. (2023)
Overcoming high homology to detect variation in *CYP21A2* with whole-genome sequencing in DRAGEN by Illumina Inc. (2023)
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions by Olson et al (2020)
Unveiling Illumina Connected Annotations: A breakthrough in genomic annotation by Illumina Inc. (2024)

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.

The Cancer Dependency Map (DepMap) Cancer Cell Line Encyclopedia (CCLE) Dataset

Tutorials

DepMap Omics CCLE data on the AWS Open Data Registry by Devin McCabe

Tools & Applications

Cancer Cell Line Encyclopedia (CCLE) by Ghandi, Huang, Jané-Valbuena et al.
The Cancer Dependency Map (DepMap) by Arafeh, Shibue, Dempster et al.

Publications

Bridging the gap between cancer cell line models and tumours using gene expression data by Noorbakhsh, Vazquez & McFarland
Genetic dependencies associated with transcription factor activities in human cancer cell lines by Thatikonda, Supper, Wachter et al.
Integrated cross-study datasets of genetic dependencies in cancer by Pacini, Dempster, Boyle et al.
Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors by Sanders, Chandra, Zebarjadi et al.
Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, Huang, Jané-Valbuena et al.
Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal by Krill-Burger, Dempster, Borah et al.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks by Ben Guebila, Wang, Lopes-Ramos et al.
The present and future of the Cancer Dependency Map by Arafeh, Shibue, Dempster 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.

ICGC on AWS

Tutorials

AWS Pancancer Workflow Launcher by Solomon Shorser

Publications

Serratus: Ultra-deep Search for Novel Viruses - Versioned Data Release

Tools & Applications

Serratus Explorer by Serratus Team
Tantalus: An R Package for exploration of Serratus data by Serratus Team

Publications

coronaSPAdes. From biosynthetic gene clusters to RNA viral assemblies by Meleshko D., Hajirasouliha I., and Korobeynikov A. (2021)
Diversification of mammalian deltaviruses by host shifting by Bergner L.M., Orton R.J., et al (2021)
Petabase-scale sequence alignment catalyses viral discovery by Edgar R., Taylor J., Lin V., et al (2021)
Ribovirus classification by a polymerase barcode sequence by Babaian A., and Edgar R. (2021)

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)

ONT Methylation Benchmarking Datasets

Tutorials

Methylation calling using ONT methylation benchmarking dataset by Onkar Kulkarni
Running Benchmarking Pipeline (Nextflow/Snakemake) on an Example Dataset using AWS by Onkar Kulkarni

Publications

Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation by Kulkarni et al.

DNAStack COVID19 SRA Data

Tutorials

Viral lineage assignment by Heather Ward
AWS BatchAmazon EC2Amazon S3

Tools & Applications

Viral AI by DNAstack

Somatic Mosaicism across Human Tissues (SMaHT)

Tools & Applications

Somatic Mosaicism across Human Tissues Data Portal by SMaHT Data Analysis Center (DAC)

Publications

The Somatic Mosaicism across Human Tissues Network by Coorens T, Oh J, Choi Y, Lim N, Zhao B, Voshall A et al.

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

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

iHART Whole Genome Sequencing Data Set

Publications

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks by Ruzzo et al. (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.