KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Online Publication Date2015-10-25
Print Publication Date2016-02
Permanent link to this recordhttp://hdl.handle.net/10754/581472
MetadataShow full item record
AbstractNext-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.
CitationV-GAP: Viral genome assembly pipeline 2015 Gene
- DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque.
- Authors: Kot W, Vogensen FK, Sørensen SJ, Hansen LH
- Issue date: 2014 Feb
- Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.
- Authors: Karamitros T, van Wilgenburg B, Wills M, Klenerman P, Magiorkinis G
- Issue date: 2018 Aug 2
- Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.
- Authors: Lin HH, Liao YC
- Issue date: 2015
- Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.
- Authors: Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA
- Issue date: 2017 May 4
- Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.
- Authors: Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE
- Issue date: 2011 Nov