NEW: We have published a protocol for analysing tandem repeats from short-read sequencing data, which includes the use of STRipy's resources. Find it in the journal of Current Protocols in Bioinformatics.
STRipy's online resources comprise a curated database for short tandem repeats (STRs) and online tools that support the utilisation of ExpansionHunter software.
STRs database houses information about known pathogenic STR loci. For each locus, it provides concise research paper summary, details like coordinates for various reference genomes (hg19, hg38 & hs1), motifs, repeat ranges (normal, intermediate, pathogenic) and associated diseases, including their onset and inheritance modes. Moreover, population-wide repeat frequencies are provided for each locus.
ExpansionHunter online tools contain firstly, the Variant catalogue creator that allows to generate variant catalogues compatible with ExpansionHunter software. This tool covers all loci in the STRs database, supports main human reference genomes and includes pre-defined off-target regions that enables to genotype long repeats. Catalogue content can be customised - either select specific loci or utilise predefined groups, such as those associated with neurological diseases, childhood/adult onset conditions, repeats in coding regions, UTRs or introns. Secondly, Results analyser processes ExpansionHunter output files to generate graphical reports. These reports make it very easy to notice any results that are in intermediate or pathogenic range as well as those which are population outliers.
STRipy's software includes a graphical application for genotyping short tandem repeats in the simplest way that uses cloud-genotyping (download links below), and also a command-line version named STRipy-pipeline that is available for a large scale analysis of STRs, supporting parallel processing and newest telomere-to-telomere reference genome.
STRipy-pipeline is the most up-to-date tool and allows the genotyping of any STR locus in an aligned Illumina WGS/WES or targeted sequencing file. STRipy also detects whether an allele is in the pathogenic range for 65 diseases caused by 61 STR loci in 58 genes and provides the distributions of alleles in healthy populations (including the reference missing XYLT1 locus). Find more information on the About page and the publication. Feel free to contact the author at any time for inquiries or feedback.