Registry of Open Data on AWS

Usage examples for all datasets listed in the Registry of Open Data on AWS tagged with fast5.

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.

Human PanGenomics Project

Publications

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

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

ONT Dataset Tutorials by EPI2MELabs

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

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.