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  3. Genome annotation
  4. Repetitive DNA
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A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal).

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Input format:
FASTA, FASTQ
Operating system:
Unix/Linux
Programming languages:
C
License:
GNU General Public License version 2.0
Computer skills:
Advanced
Stability:
Stable
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Publications

  • (Iqbal et al., 2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature genetics.
    PMID: 22231483

Classification

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