Fig. 1

LUSTR pipeline and modules. LUSTR distinguishes itself from other existing pipelines or tools in the following aspects: (1) A “finder” module to standardize extraction of genomic STR regions to be genotyped. The “finder” module aims to simplify the information required to target specific STRs, diminish the impact of imperfect input, and provide flexibility to allow easier user customized target lists, ranging from unbiased compilations for genome-wide scans or a small number of targeted STR sequences. (2) Instead of directly processing mapped reads (.bam files) obtained from alignment pipelines not necessarily optimized for STRs, LUSTR de novo remaps the raw reads (.fastq files) to STR references defined in the “finder” module, with parameters adjusted specifically for STR calling to enhance the performance. We provide an “extractor” module to retrieve reads from the.bam file if raw reads are not available. This remapping step and the “finder” module, indicated by a dashed rectangle, are unique to LUSTR and are not available in other STR calling pipelines. (3) LUSTR implements a flexible two-step strategy for STR genotyping, separating the local realignment step in the “realigner” module to incorporate reads that may have been discarded during the mapping process, and a freestanding calling step in the “caller” module which processes the realignment results to estimate the genotypes for each STR. This modular approach allows for precise tracking of reads through realignment which is critical for debugging and performance evaluation, and allows easier implementation of necessary updates or incorporation of project specific optimization. (4) The “realigner” module applies both flanking-guided and repeat-guided realignment to ensure both accuracy and sensitivity. (5) The “caller” module allows fractional multiallelic STR genotyping results amenable to the calling of germline or somatic expansions or contractions. (6) LUSTR minimizes the prerequisites and only requires pre-installations of samtools and bwa