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Cortex specifications


Unique identifier OMICS_00056
Name Cortex
Alternative names McCortex, cortex_var
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ, SAM, BAM & CRAM
Operating system Unix/Linux, Mac OS
Programming languages C
License GNU General Public License version 2.0, MIT License
Computer skills Advanced
Version 0.2
Stability Beta
Maintained Yes


No version available



  • person_outline Isaac Turner

Additional information Previous version:

Publications for Cortex

Cortex citations


Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the USA and a Clade Specific Loss of Hydrogen Sulfide Production

Front Microbiol
PMCID: 5410586
PMID: 28507536
DOI: 10.3389/fmicb.2017.00737

[…] 0 bootstrap iterations in RaxML version 8 (). This initial tree and assembly quality metrics were used to guide the selection of a reference strain FSL R8-3655 for comprehensive variant calling using cortex_var (). Cortex_var was run with the kmer sizes of 33 and 63 to identify variants across 86 S. Cerro genomes, using strain FSL R8-3655 as a reference; high quality SNPs (qtresh set at 15) were u […]


Whole genome analysis of mycobacteria from birds at the San Diego Zoo

PLoS One
PMCID: 5340394
PMID: 28267758
DOI: 10.1371/journal.pone.0173464

[…] or bacteria. The reference genomes used in the BWA read mapping were Mycobacterium avium 104, M. fortuitum DSM 46621, M. genavense ATCC 51234, and M. intracellulare MOTT-64 from the NCBI database.For Cortex_var the joint workflow with a CoordinatesOnly reference was used since it generally gave the same or a few more high-confidence variants than any of the other three workflows. The references ad […]


Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Genome Biol
PMCID: 5155386
PMID: 27964752
DOI: 10.1186/s13059-016-1090-1

[…] q suite [], using either the Iberian lynx or the domestic cat genome as references and different sets of samples. In addition, we applied the reference-free and assembly-based strategy implemented in Cortex_var []. The two procedures yielded largely concordant results but, as expected by its higher sensitivity to detect singletons, the mapping-based calling dataset yielded more variants, slightly […]


A set of powerful negative selection systems for unmodified Enterobacteriaceae

Nucleic Acids Res
PMCID: 4513841
PMID: 25800749
DOI: 10.1093/nar/gkv248

[…] e manufacturer's recommendations. This library was sequenced on a HiSeq 2000 (2 × 76 bp reads), yielding 5 680 917 read pairs (∼170× coverage). After quality filtering, fastq files were analyzed with cortex_var (version from the Cortex package () using a joint analysis with UTI89 (NCBI accession number NC_007946) as the reference genome; the resulting VCF files indicated the known deleti […]


A single natural nucleotide mutation alters bacterial pathogen host tropism

Nat Genet
PMCID: 4824278
PMID: 25685890
DOI: 10.1038/ng.3219

[…] tic analyses. Genes specific to rabbit ST121 isolates were identified by comparing the sequenced rabbit isolate genome sequences to the human ST121 sequences using the print_novel_contigs function of cortex_var v1.0.5.20. […]


Identifying and Classifying Trait Linked Polymorphisms in Non Reference Species by Walking Coloured de Bruijn Graphs

PLoS One
PMCID: 3607606
PMID: 23536903
DOI: 10.1371/journal.pone.0060058

[…] han the more conservative approach adopted by the Cortex bubble caller. To confirm this was the case, we used the same Bur-0, Tsu-1 and Ler-1 (50×) Arabidopsis reads as input to the latest version of Cortex_var ( and verified the bubbles it output using the same method as for Bubbleparse. At optimal kmer size for each tool, Cortex_var called a lower percentage of the canonical SNPs than B […]


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Cortex institution(s)
Wellcome Trust Centre for Human Genetics, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK; European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
Cortex funding source(s)
Supported by the Wellcome Trust (grant numbers 090532/Z/09/Z and 100956/Z/13/Z), Wellcome Trust Research Studentship award (097310/Z/11/Z), a PhD studentship from the BBSRC and a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (grant 102541/Z/13/Z).

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