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

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.

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Abbreviations

ACC:

accuracy

BAC:

bacterial artificial chromosome

CE:

compression-expansion

FCD:

fragment coverage distribution

FN:

false negative

FP:

false positive

MCC:

Matthews correlation coefficient

NCBI:

National Center for Biotechnology Information

PDBG:

paired de Bruijn graphs

PE:

paired end

SBS:

sequencing-by-synthesis

SE:

single end

SRA:

sequence read archive

TN:

true negative

TP:

true positive

WGS:

whole genome shotgun

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Acknowledgements

We are thankful to Rohit Chauhan for his help during the analysis. VC is thankful to DST for SRF-INSPIRE fellowship, RK is thankful to DBT-BINC. We are thankful to all the researchers who provided their valuable data as an open access resource. The manuscript has IHBT communication ID: 3959. This work was supported under project funding BSC-121 (CSIR-12th FYP GENESIS project).

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Correspondence to Ravi Shankar.

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[Chawla V, Kumar R and Shankar R 2016 Identifying wrong assemblies in de novo short read primary sequence assembly contigs. J. Biosci.]

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Chawla, V., Kumar, R. & Shankar, R. Identifying wrong assemblies in de novo short read primary sequence assembly contigs. J Biosci 41, 455–474 (2016). https://doi.org/10.1007/s12038-016-9630-0

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  • DOI: https://doi.org/10.1007/s12038-016-9630-0

Keywords

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