Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing

Jha, A.; Bohaczuk, S. C.; Mao, Y.; Ranchalis, J.; Mallory, B. J.; Min, A. T.; Hamm, M. O.; Swanson, E.; Finkbeiner, C.; Li, T.; Whittington, D.; Noble, W. S.; Stergachis, A. B.; Vollger, M. R.

doi:10.1101/2023.04.20.537673

bioRxiv · 10.1101/2023.04.20.537673

Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing

Jha, A.·Bohaczuk, S. C.·Mao, Y.·Ranchalis, J.·Mallory, B. J.·Min, A. T.·Hamm, M. O.·Swanson, E.·Finkbeiner, C.·Li, T.·Whittington, D.·Noble, W. S.·Stergachis, A. B.·Vollger, M. R.

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Abstract

Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as co-processing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools. Here, we introduce fibertools, a state-of-the-art toolkit that features a semi-supervised convolutional neural network for fast and accurate identification of m6A-marked bases using PacBio single-molecule long-read sequencing, as well as the co-processing of long-read genetic and epigenetic data produced using either PacBio or Oxford Nanopore sequencing platforms. We demonstrate accurate DNA-m6A identification (>90% precision and recall) along >20 kilobase long DNA molecules with a [~]1,000-fold improvement in speed. In addition, we demonstrate that fibertools can readily integrate genetic and epigenetic data at single-molecule resolution, including the seamless conversion between molecular and reference coordinate systems, allowing for accurate genetic and epigenetic analyses of long-read data within structurally and somatically variable genomic regions.

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Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Finkbeiner, C., Li, T., Whittington, D., Noble, W. S., Stergachis, A. B., Vollger, M. R.. 2023-04-21. Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing. https://doi.org/10.1101/2023.04.20.537673

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