Short tandem repeats (STRs), or microsatellites, are the class of repeat sequences that have repeat units of up to 6 bp directly adjacent to each other. STRs are generally more polymorphic than other kinds of variation such as sequence copy number and single-nucleotide…
Desktop app
G T A T C G C T A Pindel Pindel

Pindel

Detects breakpoints of large deletions, medium sized insertions, inversions,…

Detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequence data. Pindel…

Desktop app
G T A T C G C T A DELLY DELLY

DELLY

An integrated structural variant prediction method that can detect deletions,…

An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel…

Desktop app
G T A T C G C T A lobSTR lobSTR

lobSTR

A tool for profiling Short Tandem Repeats (STRs) from high throughput…

A tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

Desktop app
G T A T C G C T A RepeatSeq RepeatSeq

RepeatSeq

Determines genotypes for microsatellite repeats in high-throughput sequencing…

Determines genotypes for microsatellite repeats in high-throughput sequencing data.

Desktop app
G T A T C G C T A AGE AGE

AGE

An algorithm for the correct alignment of two nucleotide sequences containing…

An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e. deletion, insertion, tandem duplication or inversion. The algorithm does not require the adjustment or…

Desktop app
G T A T C G C T A TRhist TRhist

TRhist

A tool for finding significant tandem repeats using short reads.

A tool for finding significant tandem repeats using short reads.

Desktop app
G T A T C G C T A GenoTan GenoTan

GenoTan

A free tool to identify length variation of microsatellites from short sequence…

A free tool to identify length variation of microsatellites from short sequence reads.

Desktop app
G T A T C G C T A HighSSR HighSSR

HighSSR

Predicts microsatellites with Tandem Repeats Finder (TRF).

Predicts microsatellites with Tandem Repeats Finder (TRF).

Web app
G T A T C G C T A ATRHUNTER ATRHUNTER

ATRHUNTER

Detects and displays approximate tandem repeats in genomic sequences. ATRHUNTER…

Detects and displays approximate tandem repeats in genomic sequences. ATRHUNTER is based on a flexible statistical model which allows a wide range of definitions of approximate tandem repeats.

Desktop app
G T A T C G C T A SSR_pipeline SSR_pipeline

SSR_pipeline

A Bioinformatic Infrastructure for Identifying Microsatellites From Paired-End…

A Bioinformatic Infrastructure for Identifying Microsatellites From Paired-End Illumina High-Throughput DNA Sequencing Data. All modules are implemented in the Python programming language and can…

Desktop app
G T A T C G C T A BreaKmer BreaKmer

BreaKmer

An approach that uses a 'kmer' strategy to assemble misaligned…

An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair…

Desktop app
G T A T C G C T A smrt pipeline smrt pipeline

smrt pipeline

Enables recovery of high identity allele structures for the sequence regions…

Enables recovery of high identity allele structures for the sequence regions whose length was confirmed by Polymerase Chain Reaction (PCR) from cell line genomic DNA. smrt_pipeline is a method for…

Desktop app
G T A T C G C T A FDSTools FDSTools

FDSTools

Allows the analysis of massively parallel sequencing data with the ability to…

Allows the analysis of massively parallel sequencing data with the ability to recognise and correct short tandem repeat (STR) stutter. FDSTools uses a database of reference samples to determine…

Desktop app
G T A T C G C T A Targeted… Targeted characterisation of Short Structural…

TSSV Targeted characterisation of Short Structural Variation

A method for targeted profiling of short tandem repeats (STRs) that reports a…

A method for targeted profiling of short tandem repeats (STRs) that reports a full spectrum of all observed genomic variants along with their respective abundance. TSSV can accurately profile and…

Desktop app
G T A T C G C T A Haplotype inference… Haplotype inference and phasing for Short Tandem…

HipSTR Haplotype inference and phasing for Short Tandem Repeats

A haplotype-based method for robustly genotyping, haplotyping, and phasing…

A haplotype-based method for robustly genotyping, haplotyping, and phasing short tandem repeats (STRs) from whole genome sequencing data. HipSTR uses a multitude of inference techniques that…

Desktop app
G T A T C G C T A popShortTandemRepeats popShortTandemRepeats

popSTR popShortTandemRepeats

A microsatellite genotyper optimized for Illumina capable of studying…

A microsatellite genotyper optimized for Illumina capable of studying microsatellite variation within all individuals of a population simultaneously. PopSTR starts by determining a set of informative…

Desktop app
G T A T C G C T A Hybrid Structural… Hybrid Structural variant Assembly

HySA Hybrid Structural variant Assembly

Integrates sequencing reads from next-generation sequencing (NGS) and…

Integrates sequencing reads from next-generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By…

Desktop app
G T A T C G C T A ALPHA satellite… ALPHA satellite CENTromeric AUtomated Repeat…

Alpha-CENTAURI ALPHA satellite CENTromeric AUtomated Repeat Identification

A python-based workflow for characterizing satellite sequence variants in long…

A python-based workflow for characterizing satellite sequence variants in long read datasets. This automated method is useful in reporting de novo higher order repeat sequence organization and…

Desktop app
G T A T C G C T A Assisted Automated… Assisted Automated Assembler of Repeat Families

AAARF Assisted Automated Assembler of Repeat Families

Identifies sequence overlaps in small shotgun sequence datasets and walks them…

Identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome. Testing of AAARF in maize…

Desktop app
G T A T C G C T A MetaSV MetaSV

MetaSV

An integrated structural variation (SV) caller which leverages multiple…

An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of…

Desktop app
G T A T C G C T A ReAd Pair spliT… ReAd Pair spliT Read-Structural Variant

RAPTR-SV ReAd Pair spliT Read-Structural Variant

A program designed to process previously aligned, Illumina Paired-end whole…

A program designed to process previously aligned, Illumina Paired-end whole genome sequence data to identify structural variants such as deletions, insertions and tandem duplications. Simulations…

Desktop app
G T A T C G C T A Sample Heterogeneity… Sample Heterogeneity Estimation and Assembly by…

SHEAR Sample Heterogeneity Estimation and Assembly by Reference

A tool for next-generation sequencing data analysis that predicts SVs, accounts…

A tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to…

Desktop app
G T A T C G C T A Short Tandem Repeat… Short Tandem Repeat allele identification tool…

STRait Razor Short Tandem Repeat allele identification tool Razor

A software tool to detect short tandem repeat (STR) alleles in massively…

A software tool to detect short tandem repeat (STR) alleles in massively parallel sequencing (MPS) raw data. The method of detection used by STRait Razor allows it to make reliable allele calls for…

Desktop app
G T A T C G C T A Meerkat Meerkat

Meerkat

To characterize the mutational spectrum of somatic SVs in cancer, it is…

To characterize the mutational spectrum of somatic SVs in cancer, it is important to identify both simple (e.g., deletion, insertion, and inversion) and complex SVs at base-pair resolution. Meerkat…

Desktop app
G T A T C G C T A iMSAT iMSAT

iMSAT

A python program that uses the polymorphism data obtained from mapping…

A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.

Desktop app
G T A T C G C T A PacmonSTR PacmonSTR

PacmonSTR

A reference-based probabilistic approach to identify the TR region and estimate…

A reference-based probabilistic approach to identify the TR region and estimate the number of these TR elements in long DNA reads.

Web app
G T A T C G C T A QDD QDD

QDD

An open access program providing a user-friendly tool for microsatellite…

An open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences.

Desktop app
G T A T C G C T A VNTRseek VNTRseek

VNTRseek

Pipeline for discovery of minisatellite DNA tandem repeats (TR) variants.

Pipeline for discovery of minisatellite DNA tandem repeats (TR) variants.

Desktop app
Web app
G T A T C G C T A Imperfect… Imperfect Microsatellite Extractor

IMEx Imperfect Microsatellite Extractor

Online and stand-alone tool for extracting perfect, imperfect and compound…

Online and stand-alone tool for extracting perfect, imperfect and compound SSRs/Microsatellites from DNA Sequences.

Desktop app
G T A T C G C T A Pair Read Informed… Pair Read Informed Split Mapper

PRISM Pair Read Informed Split Mapper

A method that identifies SVs and their precise breakpoints from whole-genome…

A method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling…

Desktop app
G T A T C G C T A Short Tandem Repeat… Short Tandem Repeat Variation Identification from…
Desktop app
G T A T C G C T A detecttd detecttd

detecttd

Detects tandem duplications in sequencing reads. detecttd is written in Python…

Detects tandem duplications in sequencing reads. detecttd is written in Python and requires NCBI Blast standalone.

Desktop app
G T A T C G C T A MISA MISA

MISA

This tool allows the identification and localization of perfect microsatellites…

This tool allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.

Desktop app
G T A T C G C T A palfinder palfinder

palfinder

A perl script that finds microsatellite repeat elements directly from raw 454…

A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.

Desktop app
G T A T C G C T A SSRLocator SSRLocator

SSRLocator

A tool for detection and characterization of micro- and minisatellites in DNA…

A tool for detection and characterization of micro- and minisatellites in DNA sequences.

Desktop app
G T A T C G C T A vcf2MSAT vcf2MSAT

vcf2MSAT

A python program to identify microsatellite repeat regions based on known…

A python program to identify microsatellite repeat regions based on known polymorphisms identified in a ".vcf" report after using SAMtools to analyze next-generation sequencing files.

Desktop app
G T A T C G C T A Geneious… Geneious Microsatellite Plugin

Geneious Microsatellite Plugin

This free Geneious plugin imports ABI fragment analysis files and allows you…

This free Geneious plugin imports ABI fragment analysis files and allows you to visualize traces, fit ladders, call peaks, predict bins, display alleles in a tabular format and export your data.

Desktop app
G T A T C G C T A GMATo GMATo

GMATo

A novel tool for the identification and analysis of microsatellites in large…

A novel tool for the identification and analysis of microsatellites in large genomes.

Desktop app
G T A T C G C T A INVERTER Deprecated INVERTER

INVERTER

A de novo exact match tandem repeat finder which main advantage is without the…

A de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a…

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