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Improving Bacterial Genome Assembly Using a Test of Strand Orientation

Grant Greenberg, Ilan Shomorony
doi: https://doi.org/10.1101/2022.07.06.499059
Grant Greenberg
1Dept. of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
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  • For correspondence: gcgreen2@illinois.edu
Ilan Shomorony
1Dept. of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
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Abstract

The complexity of genome assembly is due in large part to the presence of repeats. In particular, large reverse-complemented repeats can lead to incorrect inversions of large segments of the genome. To detect and correct such inversions in finished bacterial genomes, we propose a statistical test based on tetranucleotide frequency (TNF), which determines whether two segments from the same genome are of the same or opposite orientation. In most cases, the test neatly partitions the genome into two segments of roughly equal length with seemingly opposite orientations. This corresponds to the segments between the DNA replication origin and terminus, which were previously known to have distinct nucleotide compositions. We show that, in several cases where this balanced partition is not observed, the test identifies a potential inverted misassembly, which is validated by the presence of a reverse-complemented repeat at the boundaries of the inversion. After inverting the sequence between the repeat, the balance of the misassembled genome is restored. Our method identifies 31 potential misassemblies in the NCBI database, several of which are further supported by a reassembly of the read data.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/gcgreenberg/Oriented-TNF.git

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 July 06, 2022.
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Improving Bacterial Genome Assembly Using a Test of Strand Orientation
Grant Greenberg, Ilan Shomorony
bioRxiv 2022.07.06.499059; doi: https://doi.org/10.1101/2022.07.06.499059
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Improving Bacterial Genome Assembly Using a Test of Strand Orientation
Grant Greenberg, Ilan Shomorony
bioRxiv 2022.07.06.499059; doi: https://doi.org/10.1101/2022.07.06.499059

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