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Karyon is a pipeline for the assembly and analysis of highly heterozygous genomes. It uses redundans (Pryszcz & Gabaldón, 2016) to reduce heterozygosity during the assembly process, and then maps the original libraries against the reduced assembly to analyze the distribution of heterozygous regions. With this information, it generates a series of plots that can aid researchers to generate informed hypotheses with regard of the architecture of their genomes.
The pipeline contains a principal script (karyon.py) with different modules.
(1) karyon.py -> complete pipeline, including genome assembly, assembly reduction, SNP calling and plot generation (2) prepare_libraries.py -> karyon dependency. It uses Trimmomatic () to trim input libraries before genome assembly. (3) spades_recipee.py -> Karyon dependency. It generates a file that launches dipSPAdes () with the input. (4) varcall_recipee.py -> Karyon dependency. It generates a file that launches all steps in the SNP calling pipeline. (5) karyonplots.py -> Karyon dependency. It generates all the plots as part of the Karyon pipeline. (6) allplots.py -> Standalone version of karyonplots.py. It allows the user to input karyon results to generate the plots again.
Why should I use Karyon? To-Do
When should I use Karyon? To-Do
What type of data do I need to run the whole Karyon pipeline? To-Do
In which version of python is Karyon implemented?
Karyon is implemented in python 2.7 and 3.5. You just need to choose the version you prefer.
I do not have an operating system compatible with Karyon. How can I run it?
Karyon is implemented in Docker. Install Docker in your computer and you will be able to obtain the proper environment to run Karyon. Check Karyon manual for more details.