Journal article

Identifying wrong assemblies in de novo short read primary sequence assembly contigs

Chawla V, Kumar R, Shankar R ...see all

Journal of Biosciences, vol. 41, issue 3 (2016) pp. 455-474 Published by Springer India

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Abstract

With the advent of short-reads-based genome sequencing approaches, large number of organisms are being sequenced all over the world. Most of these assemblies are done using some de novo short read assemblers and other related approaches. However, the contigs produced this way are prone to wrong assembly. So far, there is a conspicuous dearth of reliable tools to identify mis-assembled contigs. Mis-assemblies could result from incorrectly deleted or wrongly arranged genomic sequences. In the present work various factors related to sequence, sequencing and assembling have been assessed for their role in causing mis-assembly by using different genome sequencing data. Finally, some mis-assembly detecting tools have been evaluated for their ability to detect the wrongly assembled primary contigs, suggesting a lot of scope for improvement in this area. The present work also proposes a simple unsupervised learning-based novel approach to identify mis-assemblies in the contigs which was found performing reasonably well when compared to the already existing tools to report mis-assembled contigs. It was observed that the proposed methodology may work as a complementary system to the existing tools to enhance their accuracy.

Author-supplied keywords

  • Assembly validation
  • clustering
  • contigs
  • de novo assembly
  • mis-assembly
  • next generation sequencing
  • reads

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Authors

  • Vandna Chawla

  • Rajnish Kumar

  • Ravi Shankar

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