High-throughput microbial population genomics using the Cortex variation assembler

Bioinformatics
Zamin IqbalGil McVean

Abstract

We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads. http://cortexassembler.sourceforge.net (GPLv3 license). zam@well.ox.ac.uk, mcvean@well.ox.ac.uk Supplementary data are available at Bioinformatics online.

References

May 23, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael M MwangiAlexander Tomasz
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Oct 8, 2009·Bioinformatics·Jacob F DegnerJonathan K Pritchard
Jan 11, 2012·Nature Genetics·Zamin IqbalGil McVean
Mar 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Bernadette C YoungDaniel J Wilson

Citations

Feb 26, 2014·BMC Bioinformatics·Vincent RanwezJacques David
Jan 18, 2014·Nature Reviews. Genetics·David SimsChris P Ponting
Jul 26, 2014·Emerging Infectious Diseases·Henk C den BakkerWilliam J Wolfgang
Jan 17, 2016·Annual Review of Food Science and Technology·Xiangyu DengRene S Hendriksen
Jun 27, 2015·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Yancy LoSebastian Zöllner
May 9, 2015·Bioinformatics·Adrian Baez-OrtegaCarlos Flores
Feb 17, 2015·Nature Genetics·David VianaJosé R Penadés
Mar 20, 2018·Bioinformatics·Isaac TurnerGil McVean
Aug 9, 2018·PloS One·Claes Søndergaard WassmannJanne Kudsk Klitgaard
Jun 28, 2015·Applied and Environmental Microbiology·Matthew J StasiewiczHenk C den Bakker
Aug 28, 2013·Nature Reviews. Microbiology·Martin C J MaidenNoel D McCarthy
Sep 28, 2019·Molecular Biology and Evolution·Jesper EisfeldtAnna Lindstrand

Related Concepts

Computer Programs and Programming
Variation (Genetics)
Single Nucleotide Polymorphism
Genomics
INDEL Mutation
Metagenomics
Cerebral Cortex
Genome
License
Computer Software

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