Journal Article

STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

Ravenscroft, Gianina, Beecroft, Sarah J., Davis, Mark, LaCroix, Amy J., Pedersen, Brent S., Roxburgh, Richard H., Laing, Nigel G., Dashnow, Harriet, Hiatt, Laurel, Rodrigues, Miriam J., Lamont, Phillipa, Quinlan, Aaron R., Mefford, Heather C., Brown, Joe

2022

Overview

Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for “novel” STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling .

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animal Genetics and Genomics / Ataxia / Bioinformatics / Biomedical and Life Sciences / Disease / DNA / DNA methylation / DNA sequencing / Evolutionary Biology / genome / Genomes / High-Throughput Nucleotide Sequencing / Human Genetics / Life Sciences / Method / Microbial Genetics and Genomics / Microsatellite Repeats / Patients / Plant Genetics and Genomics / Sequence Analysis, DNA / Short tandem repeats