RepeatSeq statistics

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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

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Documentation


Maintainer


  • person_outline David Mittelman <>

Publication for RepeatSeq

RepeatSeq in publications

 (11)
PMCID: 5941971
PMID: 29770143
DOI: 10.3389/fgene.2018.00155

[…] 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., ), […]

PMCID: 5855144
PMID: 29593777
DOI: 10.3389/fgene.2018.00073

[…] (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 […]

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

[…] from trf, mreps and repeatmasker. the genomic locations of ssr repeats were extracted from the repet annotation result and used to create a ssr region file to be used for genotyping using repeatseq., whole genome genotyping of ssr repeats was done using repeatseq v0.8.2. to do this, paired-end illumina reads from two other p. cinnamomi isolates from australia and new zealand […]

PMCID: 5734450
PMID: 29276372
DOI: 10.1177/1176935117746644

[…] a heterozygote genotype with 14- and 15-base-pair alleles, respectively. the genotype “15|15” indicates a homozygote genotype with 2 copies of the 15-base-pair alleles., 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: […]

PMCID: 5322674
PMID: 28228131
DOI: 10.1186/s12920-017-0246-5

[…] 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 […]


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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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