CRANE Evaluation and Training Dataset

This is the evaluation dataset used for the tool CRANE, found at https://github.com/STORMgroup/CRANE.This was derived from 3 datasets:1) The ATCC_25922__202309 E. coli sample used in Hall et al., [1]. Download: https://figshare.unimelb.edu.au/ndownloader/files/454086282) The D. Melanogaster sample in the Oxford Nanopore Open Data project [2]. s3 download: s3://ont-open-data/contrib/melanogaster_bkim_2023.01/flowcells/D.melanogaster.R1041.400bps/D_melanogaster_1/20221217_1251_MN20261_FAV70669_117da01a/fast5/

3) The Human sample HG002 from the Oxford Nanopore Open Data: Sequencing Genome in a Bottle samples [3]. s3 download: s3://ont-open-data/giab_2023.05/flowcells/hg002/20230424_1302_3H_PAO89685_2264ba8c/pod5_pass/

References:

[1] Hall, M. B., Wick, R. R., Judd, L. M., Nguyen, A. N., Steinig, E. J., Xie, O., Davies, M., Seemann, T., Stinear, T. P., & Coin, L. (2024). Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. eLife, 13, RP98300. https://doi.org/10.7554/eLife.98300

[2] Oxford Nanopore Technologies, “Oxford Nanopore Open Data: Drosophila melanogaster sequencing,” https://labs.epi2me.io/open-data-dmelanogaster-bkim/, 2023, accessed via s3://ont-open-data/contrib/melanogaster_bkim_2023.01/.[3] Oxford Nanopore Technologies, “Oxford Nanopore Open Data: Sequencing Genome in a Bottle samples,” https://epi2me.nanoporetech.com/giab-2023.05/, 2023, accessed via s3://ont-open-data/giab_2023.05/.