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Errors in long-read assemblies can critically affect protein prediction

Nature Biotechnology volume 37, pages 124–126 (2019)Cite this article

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To the Editor — Long-read, single molecule sequencing technologies are now routinely used to sequence and assemble the human genome1,2,3. These studies represent an important advance and highlight the value of using long-read technologies to aid genome assembly—particularly in the complex regions that have challenged short-read methods for over a decade. However, even after multiple rounds of correction, long-read assemblies can contain errors in protein coding regions that can substantially alter, and often truncate, protein predictions.

Cheap, high-throughput short-read sequencing technologies4 have revolutionized biological research5. However, these technologies often result in incomplete and highly fragmented assemblies6, making their application to large, complex genome assembly challenging. It has long been realized7 that accurate assembly requires reads that are longer than the longest repeat region, with sufficient depth and accuracy to detect overlaps between those reads.

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Acknowledgements

This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; BB/P013732/1).

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  1. Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, UK

    Mick Watson & Amanda Warr

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  1. Mick Watson
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  2. Amanda Warr
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Correspondence to Mick Watson.

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The authors declare no competing interests.

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Editor’s Note: This article has been peer-reviewed.

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Watson, M., Warr, A. Errors in long-read assemblies can critically affect protein prediction. Nat Biotechnol 37, 124–126 (2019). https://doi.org/10.1038/s41587-018-0004-z

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