Garvan Institute Long Read Sequencing Benchmark Data

Description

The dataset contains reference samples that will be useful for benchmarking and comparing bioinformatics tools for genome analysis. Examples include: NA12878 (HG001) and NA24385 (HG002) sequenced on an Oxford Nanopore Technologies (ONT) PromethION using the latest R10.4.1 flowcells; and, UHR RNA (direct-RNA) on an ONT PromethION using the latest RNA004 flowcells. Raw signal data output by the sequencer is provided for these datasets in BLOW5 format, and can be rebasecalled when basecalling software updates bring accuracy and feature improvements over the years. Raw signal data is not only for rebasecalling, but also can be used for emerging bioinformatics tools that directly analyse raw signal data. We also provide the basecalled data alongside the raw signal data.

Update Frequency

We plan to extend this open dataset with additional samples, including sequencing runs from vendors other than ONT. We will continue to provide updated basecalls when there is a major update to the basecalling software.

License

CC BY-NC 4.0

Documentation

https://github.com/GenTechGp/gtgseq

Managed By

Genomic Technologies Group, Garvan Institute of Medical Research (https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab)

See all datasets managed by Genomic Technologies Group, Garvan Institute of Medical Research (https://www.garvan.org.au/research/labs-groups/genomic-technologies-lab).

Contact

gtgseq team

How to Cite

Garvan Institute Long Read Sequencing Benchmark Data was accessed on DATE from https://registry.opendata.aws/gtgseq. Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al. Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40, 1026–1029 (2022). https://doi.org/10.1038/s41587-021-01147-4

Usage Examples

Tutorials

• Directly processing on an s3fs mount by Hasindu Gamaarachchi
  
• Fetching subsets with slow5curl and samtools by Bonson Wong
  

Tools & Applications

• buttery-eel: The buttery eel - a slow5 guppy basecaller wrapper by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Slow5curl: library and tool for accessing remote BLOW5 files. by Wong, B., et al.
  
• Slow5lib: toolkit slow5lib is a software library for reading & writing SLOW5 files. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Slow5tools: toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  

Publications

• Accelerated nanopore basecalling with SLOW5 data format. by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Fast nanopore sequencing data analysis with SLOW5. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Flexible and efficient handling of nanopore sequencing signal data with slow5tools. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  
• Streamlining remote nanopore data access with slow5curl by Wong, B., Ferguson, J.M., Do, J.Y. et al.