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Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful

View ORCID ProfileAmatur Rahman, Paul Medvedev
doi: https://doi.org/10.1101/2022.01.20.477068
Amatur Rahman
1Department of Computer Science and Engineering, The Pennsylvania State University
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Paul Medvedev
1Department of Computer Science and Engineering, The Pennsylvania State University
2Department of Biochemistry and Molecular Biology, The Pennsylvania State University
3Huck Institutes of the Life Sciences, The Pennsylvania State University
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  • For correspondence: pzm11@psu.edu
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Abstract

Recent assemblies by the T2T and VGP consortia have achieved significant accuracy but required a tremendous amount of effort and resources. More typical assembly efforts, on the other hand, still suffer both from mis-assemblies (joining sequences that should not be adjacent) and from under-assemblies (not joining sequences that should be adjacent). To better understand the common algorithm-driven causes of these limitations, we investigated the unitig algorithm, which is a core algorithm at the heart of most assemblers. We prove that, contrary to popular belief, even when there are no sequencing errors, unitigs are not always safe (i.e. they are not guaranteed to be substrings of the sequenced genome). We also prove that the unitigs of a bidirected de Bruijn graph are different from those of a doubled de Bruijn graph and, contrary to our expectations, result in under-assembly. Using experimental simulations, we then confirm that these two artifacts exist not only in theory but also in the output of widely used assemblers. In particular, when coverage is low then even error-free data results in unsafe unitigs; also, unitigs may unnecessarily split palindromes in half if special care is not taken. To the best of our knowledge, this paper is the first to theoretically predict the existence of these assembler artifacts and confirm and measure the extent of their occurrence in practice.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 06, 2022.
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Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful
Amatur Rahman, Paul Medvedev
bioRxiv 2022.01.20.477068; doi: https://doi.org/10.1101/2022.01.20.477068
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Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful
Amatur Rahman, Paul Medvedev
bioRxiv 2022.01.20.477068; doi: https://doi.org/10.1101/2022.01.20.477068

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