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Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci. Using simulated data, we show that TREDPARSE outperforms other available software. We sampled the full genome sequences of 12,632 individuals to an average read depth of approximately 30× to 40× with Illumina HiSeq X. We identified 138 individuals with risk alleles at 15 STR disease loci. We validated a representative subset of the samples (n = 19) by Sanger and by Oxford Nanopore sequencing. Additionally, we validated the STR calls against known allele sizes in a set of GeT-RM reference cell-line materials (n = 6). Several STR loci that are entirely guanine or cytosines (G or C) have insufficient read evidence for inference and therefore could not be assayed precisely by TREDPARSE. TREDPARSE extends the limit of STR size detection beyond the physical sequence read length. This extension is critical because many of the disease risk cutoffs are close to or beyond the short sequence read length of 100 to 150 bases.

Tiger chert was used extensively by Native American people of the Clovis lithic industry as the source material for stone tools. Although tiger chert occurs naturally only within the Bridger Formation of Southwest Wyoming, tiger chert artifacts have been found throughout the American west. This paper explores the previously unreported near-infrared fluorescence emitted from tiger chert upon visible excitation. The two objectives of this study were to demonstrate the utility of near-infrared fluorescence imaging (NIRFI) to tiger chert artifacts and to identify the chemical origin of the observed fluorescence. Tiger chert was analyzed by visible and NIRFI, SEM-EDX, ICP-OES, and fluorescence spectroscopy. NIRFI can be easily used to discriminate between tiger chert artifacts and the environment, since most materials such as soil and most rocks appear black in the resultant image. This suggests NIRFI should be utilized by archeologists at any site where tiger chert has been previously identified. Additionally, NIRFI was used to differentiate between tiger chert artifacts and an artificially weathered, recently-knapped tiger chert point, suggesting that NIRFI could be used to distinguish genuine tiger chert artifacts from counterfeits. Tiger chert fluorescence was confined to the manganese-and-iron-rich surface, suggesting the presence of desert varnish; however, red agate from the same site did not exhibit fluorescence, instead implicating tiger-chert-specific weathering. Thus, the chemical origin of fluorescence was not conclusively identified.