RGT

Alignment-free genotyping software for simple sequence repeat structures from targeted sequencing reads

Simple sequence repeat structures are often genotyped using targeted sequencing, where thousands of sequence reads from the same locus are generated. These reads are then aligned to thousands of reference sequences representing all possible repeat structures that might exist in the sample.
This method is error prone because it is likely to mistakenly genotype structures that were not identified before, as unidentified SNPs, and of course the whole process is very time consuming.

RGT identifies SSR structures from raw fastq reads, identifies and exports the gremlin alleles to the user, along with 2D plots of units counts (as electrophoresis plots). It also exports 3D plots of repeat units count vs each others in loci where there are more than one expanding repeat