STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data. It is capable of detecting novel STR expansions, that is expansions where there is no STR in the reference genome at that position (or a different repeat unit from what is in the reference). It can also detect STR expansions that are annotated in the reference genome. STRling uses kmer counting to recover mis-mapped STR reads. It then uses soft-clipped reads to precisely discover the position of the STR expansion in the reference genome.
Please see the STRling Documentation for installation and running instructions.
For more details able the algorithm check out our paper.
If using STRling, please cite:
Dashnow, H., Pedersen, B.S., Hiatt, L. et al. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol 23, 257 (2022). https://doi.org/10.1186/s13059-022-02826-4