lobSTR: A short tandem repeat profiler for personal genomes

lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times a...

lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes

Inferring short tandem repeat variation from paired-end short reads

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysi...

Genetic Variation of Informative Short Tandem Repeat (STR) Loci in an Iranian Population

In the present study, genotyping of six short tandem repeat (STR) loci including CSF1PO, D16S539, F13A01, F13B, LPL and HPRTB was performed on genomic DNA from 127 unrelated individuals from the Iranian province of Isfahan. The results indicated that the allele and genotype distributions were in accordance with Hardy-Weinberg expectations. The observed heterozygosity (Ho), expected heterozygosi...

The overdue promise of short tandem repeat variation for heritability.

Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. We review here the promise of STRs in contributing to complex trait heritability and highlight the challenges that STRs pose due to their repetitive nature. W...