Difference between revisions of "Cortex"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph | |sw summary=Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph | ||
| − | |bio domain=Genomics, | + | |bio domain=Genomics, |
| − | |bio method=Sequence assembly, Variant | + | |bio method=Sequence assembly, Variant calling, |
|created by=Mario Caccamo, Zamin Iqbal | |created by=Mario Caccamo, Zamin Iqbal | ||
|created at=University of Oxford, TGAC, EBI | |created at=University of Oxford, TGAC, EBI | ||
|maintained=Yes | |maintained=Yes | ||
|input format=FASTQ, FASTA, | |input format=FASTQ, FASTA, | ||
| − | |output format=FASTA-like, VCF, | + | |output format=FASTA-like, VCF, |
|language=C | |language=C | ||
|licence=GPLv3 | |licence=GPLv3 | ||
Latest revision as of 10:23, 25 August 2015
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Application data |
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| Created by | Mario Caccamo, Zamin Iqbal |
|---|---|
| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Sequence assembly, Variant calling |
| Created at | University of Oxford, TGAC, EBI |
| Maintained? | Yes |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | FASTA-like, VCF |
| Programming language(s) | C |
| Licence | GPLv3 |
Summary: Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to a de Bruijn graph
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Description
There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.
The methods behind Cortex have been published in Nature Genetics, "De novo assembly and genotyping of variants using colored de Bruijn graphs", http://dx.doi.org/10.1038/ng.1028
Links
References
none specified
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