Cortex
|
Application data |
|
| 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
"Error: no local variable "counter" was set." is not a number.
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
To add a reference for Cortex, enter the PubMed ID in the field below and click 'Add'.
Search for "Cortex" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
