Benchmarking tools for DNA repeat identification in diverse genomes

Abstract

Continuous progression in genomics shows that repeats are important elements of genomes that perform many regulatory and other functions. Eventually, to date, many computational tools have been developed and frequently used for the identification and analysis of genomic repeats. A single tool cannot detect all different types of repeats in diverse species rather pipeline of tools is more effective. But, the choice of such rigorous and robust tools is highly challenging. A method has been implemented to select a set of optimal tools for finding all available classes of perfect and imperfect tandem repeats including microsatellites, minisatellites, and interspersed CRISPRs in genomes. A total of 11 tools have been shortlisted using rule-based selection and then ranked by analyzing rigorousness in searching in diverse species and execution time. Tool comparison shows consistency in perfect microsatellite detection performance but significantly differ for long and imperfect repeats. A web-server has been built which provides a generic platform for various classes of repeat identification from the diverse genome using multiple tools and comparison.

VarSCAT: A computational tool for sequence context annotations of genomic variants

“…To assess our newly developed tool, we used variants based on human reference assembly GRCh38 from the ClinVar database [46], Platinum Genome [47], the National Institute of Standards and Technology’s Genome in a Bottle (GIAB) [48,49], and the 1000 Genomes Project [50,51] to study the breakpoint ambiguities of indels and small variants (1–50 bp) in STR regions. Due to the varying algorithmic parameters used in different studies for STR detection, such as the minimum length of an STR and the tolerance of mismatches and indels between STR units, the definitions of an STR may vary widely and lead to highly variable interpretations [52–54]. In our study, we restricted our analysis to perfect STRs with motif sizes of 1–6 bp based the common definitions in the literature [38,55–57].…”

“…Due to the varying algorithmic parameters used in different studies for STR detection, such as the minimum length of an STR and the tolerance of mismatches and indels between STR units, the definitions of an STR may vary widely and lead to highly variable interpretations [52][53][54]. In our study, we restricted our analysis to perfect STRs with motif sizes of 1-6 bp based the common definitions in the literature [38,[55][56][57].…”

Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (Subfamily: Caesalpinioideae)

“…This could be explained by the use of different tools to identify repetitive sequences. Das & Ghosh [72] mention that specialized programs for the identi cation of repetitive sequences often present different results depending on the algorithm used. Despite that differences between algorithms make accurate comparisons di cult, general comparisons, such as the higher number of repetitive mononucleotides among SSRs in the chloroplast genomes of distant species, are still possible [40,73,74].…”

VarSCAT: A computational tool for sequence context annotations of genomic variants

“…To assess our newly developed VarSCAT tool, we used variants based on human reference assembly GRCh38 from the ClinVar database [44], Platinum Genome [45], the National Institute of Standards and Technology's Genome in a Bottle (GIAB) [46,47], and the 1000 Genomes Project [48,49] to study the breakpoint ambiguities of indels and small variants (1-50 bp) in STR regions. Due to the varying algorithmic parameters used in different studies for STR detection, such as the minimum length of an STR and the tolerance of mismatches and indels between STR units, the definitions of an STR may vary widely and lead to highly variable interpretations [50][51][52]. In our study, we restricted our analysis to perfect STRs (except benchmarking of VarSCAT in the following section) with motif sizes of 1-6 bp based the common definitions in the literature [39,[53][54][55].…”