De novo Genome Assembly: Challenges and Solutions
Sindhu D.
Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi (110 012), India
Satish Hosakoti
Dept. of Genetics and Plant Breeding, University of Agricultural Sciences (UAS), Bangalore, Karnataka (560 065), India
Bidwan Rath*
Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi (110 012), India
Sinchana Kashyap G.S.
Dept. of Genetics and Plant Breeding, University of Agricultural Sciences (UAS), Bangalore, Karnataka (560 065), India
Basanagouda Gonal
CSB-Central Sericultural Research & Training Institute (CSR&TI), Pampore, Jammu & Kashmir (192 121), India
DOI: NIL
Keywords: De Bruijn graph, De novo genome assembly, Fast QC, Overlap layout consensus
Abstract
De novo assembly is a computational process used in genomics to reconstruct genomes from short DNA sequencing reads without a reference genome. Current article outlines the definition, steps, constraints and solutions associated with de novo assembly. De novo assembly is crucial for studying non-model organisms, identifying genetic variations and understanding evolutionary relationships. A general outline of the steps involved in de novo assembly has been provided; however, slight variations may occur based on the approach to assembly employed, whether it is overlap-layout-consensus or de Bruijn graph-based. Constraints such as sequencing errors, repetitive sequences and genome size variations pose challenges to accurate assembly. Solutions to these challenges involve employing advanced algorithms, optimizing sequencing technologies and integrating multiple data sources. Understanding and overcoming these constraints are essential for enhancing the accuracy and completeness of de novo assembly, thereby enhancing the output from various genomic studies and applications.
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Reference
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