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Protocols

RepeatSeq specifications

Information


Unique identifier OMICS_00112
Name RepeatSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
Computer skills Advanced
Version 0.8.2
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline David Mittelman

Publication for RepeatSeq

RepeatSeq citations

 (13)
library_books

A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies

2018
Front Genet
PMCID: 5941971
PMID: 29770143
DOI: 10.3389/fgene.2018.00155

[…] s type of studies.Data mining tools to detect polymorphism of TR loci in raw reads from sequencing assays are among the most useful supporting tools/resources. Examples of such data mining tools are: RepeatSeq (Highnam et al., ) lobSTR (Gymrek et al., ), ReviSTER (Tae et al., ), VNTRseek (Gelfand et al., ), myFLq (Van Neste et al., ). pSTR Finder (Lee et al., ), STR-FM (Fungtammasan et al., ), Exp […]

library_books

High Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

2018
Front Genet
PMCID: 5855144
PMID: 29593777
DOI: 10.3389/fgene.2018.00073

[…] t file (BAM format) containing only reads that realigned to each locus (tested twice) was obtained for each individual, thus increasing the confidence in the identification of the alleles.We used the RepeatSeq tool (), with parameter -M 2 (minimum sequencing quality required value) to identify and quantify the alleles from the realignment files. This tool requires a file containing the chromosome […]

library_books

New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen

2017
Sci Rep
PMCID: 5732169
PMID: 29247246
DOI: 10.1038/s41598-017-17799-9

[…] ovo pipeline identified a total of 39,141 SSR regions, 7077 of which were tri- and 3332 were tetra-repeats. Genotyping of these tri- and tetra-repeat regions on two additional available genomes using RepeatSeq revealed that 165 of the tri-repeats and 62 tetra-repeats were polymorphic between the reference and the genotyped isolates. Further filtering by manual curation of the repeats to remove imp […]

call_split

ZDHHC3 as a Risk and Mortality Marker for Breast Cancer in African American Women

2017
Cancer Inform
PMCID: 5734450
PMID: 29276372
DOI: 10.1177/1176935117746644
call_split See protocol

[…] We used the program RepeatSeq to determine the genotype of microsatellites in next-generation sequencing reads. RepeatSeq has been used in previous studies of microsatellites and is freely available: https://github.com/a […]

call_split

Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine

2017
BMC Med Genomics
PMCID: 5322674
PMID: 28228131
DOI: 10.1186/s12920-017-0246-5
call_split See protocol

[…] ng the benchmarking results as recently reported [], Scalpel INDEL calls were filtered out if they have an alternative allele coverage less than five and a Chi-Square socre greater than 10.8. Fourth, RepeatSeq (v0.8.2) was utilized to detect variants near short tandem repeats regions in the genome using default settings []. Fifth, Lumpy (v 0.2.6) and CNVnator were both used to call SVs with sizes […]

library_books

Systematic Profiling of Short Tandem Repeats in the Cattle Genome

2016
Genome Biol Evol
PMCID: 5381564
PMID: 28172841
DOI: 10.1093/gbe/evw256

[…] tection in NGS data by, among other features, carefully adjusting for high mismatch/indel levels in STRs during the mapping step (lobSTR) and guiding genotyping of STRs using informed error profiles (RepeatSeq) (; ). Targeted STR region amplification, using capture array () or single-molecule Molecular Inversion Probes (MIPSTR) (), followed by NGS has also been applied to identify human STRs. More […]

Citations

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RepeatSeq institution(s)
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA; Department of Statistics, Virginia Tech, Blacksburg, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
RepeatSeq funding source(s)
Supported by National Institutes of Health [NS079926] and NVIDIA Foundation’s ‘Compute the Cure’ program.

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