A Multi-Platform de novo Genome Assembly and Comparative Analysis for the Vibrio cholerae -HC-63A1

Abstract

De novo assembly is the process of combining short and repeated reads to large contigs and scaffolds. A contig is a set of overlapping DNA sequence that together represent consensus region of DNA. Scaffolds consist of overlapping contigs separated by gaps of unknown length. Vibrio cholerae was isolated using Next Generation Sequencing Techniques. Insilico genome assembly had been done. NGS is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. The sequence data of the new strain HC-63A1 was derived from public database, analyzed and assembled using CLC, DNAnexus, DDBJpipeline. This has led to the generation of several genome sequences based exclusively on short sequence Illumina sequence reads, recently culminating in the assembly of 3.13GB genome of Vibrio cholerae HC-63A1 from Illumina sequence reads with an average length of just 99 nucleotides . Comparative analyses involving results of CLC, Velvet, Abyss and Soap denovo tools from di_erent platforms. Among these four tools CLC genome workbench is better tool for denovo assembly.