title: High-throughput microbial population genomics using the Cortex variation assembler.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://cortexassembler.sourceforge.net (GPLv3 license).
  
  
  BACKGROUND
  zam@well.ox.ac.uk, mcvean@well.ox.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK. zam@well.ox.ac.uk
authors.forename: Zamin
authors.initials: Z
authors.lastname: Iqbal
authors.forename: Isaac
authors.initials: I
authors.lastname: Turner
authors.forename: Gil
authors.initials: G
authors.lastname: McVean
mesh_terms: D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D054643:INDEL Mutation; D056186:Metagenomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software