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Cortex

Alternative name: McCortex | cortex_var

Allows de novo genome assembly and multisample variant calling. Cortex is a modular set of multi-threaded programs for manipulating assembly graphs. Linked de Bruijn Graph (LdBG) data structure and associated algorithms are implemented as part of the software. It was used for two tasks where long-range information is likely to be beneficial: finding large differences from a reference and analysis of genomic context for drug resistance genes, which was validated using a PacBio reference assembled for the sample.

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Cortex forum

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Cortex classification

Cortex specifications

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

Cortex distribution

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No versioning.

Cortex support

Documentation

Maintainer

  • Isaac Turner <>

Additional information

http://mcveanlab.github.io/mccortex/ Previous version: http://cortexassembler.sourceforge.net/index_cortex_var.html

Credits

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Publications

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

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).

Link to literature

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