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collaborativebioinformatics / STRdust

MIT License
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Github : Add simulation strategy #30

Closed lfpaulin closed 3 years ago

lfpaulin commented 3 years ago

TODO please @DamarisLa briefly explain you method

DamarisLa commented 3 years ago

STRsimulator

Manipulation of a Referencefile in order to simulate STR!!

STRsimulator The simulator takes a haploid file as reference(.fasta) and a region file (.bed) containing information about known STR-regions as input. All of the supplied regions can be modified in

expansion (% of regions that will randomly be positive or negative expanded [0.00-1.00]),
mutation (% chance for a base to be substituted [0.00-1.00]),
number of indels (X times less likely than chance for mutation to insert or delete a base [0.00-1.00]). Further can the simulation file (.fasta) be created as
haploid [h] or
diploid [d]. If diploid is chosen,
    the percentage of regions that should get homozygous can be set [0.00-1.00].

The simulator works on assembled genomes, as well as on only one or more assembled chromosomes, if the bed-file contains such entrances likewise (anything else could run errorfree, but will not manipulate anything, as manipulations only occur in the known regions).

lfpaulin commented 3 years ago

Added to README