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Microsatellite detection software tools | Whole-genome sequencing data analysis

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…
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MISA-web
Web

MISA-web MIcroSAtellite identification tool

Can retrieve sequences from the NCBI database by specifying the corresponding…

Can retrieve sequences from the NCBI database by specifying the corresponding accession numbers in the input field. MISA-web is an extension to the command line tool MISA embedded into an easy-to-use…

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Pindel
Desktop

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…

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Meerkat
Desktop

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…

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DELLY
Desktop

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…

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lobSTR
Desktop

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.

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RepeatSeq
Desktop

RepeatSeq

Determines genotypes for microsatellite repeats in high-throughput sequencing…

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

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STRViper
Desktop
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HySA
Desktop

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…

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PRISM
Desktop

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…

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AGE
Desktop

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…

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RAPTR-SV
Desktop

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…

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TRhist
Desktop

TRhist

Finds significant tandem repeats using short reads. TRhist is a tandem repeat…

Finds significant tandem repeats using short reads. TRhist is a tandem repeat profiler that enable to sense and locate short tandem repeats (STRs) from billions of short reads. Information provided…

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GenoTan
Desktop

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.

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BreaKmer
Desktop

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…

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smrt pipeline
Desktop

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…

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popSTR
Desktop

popSTR popShortTandemRepeats

Studies microsatellite variation within all individuals of a population…

Studies microsatellite variation within all individuals of a population simultaneously. PopSTR starts by determining a set of informative reads for each marker/individual pair and computing various…

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Alpha-CENTAURI
Desktop

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…

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HighSSR
Desktop

HighSSR

Predicts microsatellites with Tandem Repeats Finder (TRF).

Predicts microsatellites with Tandem Repeats Finder (TRF).

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ProGeRF
Web
Desktop

ProGeRF Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

Extracts repetitive regions from genome and proteome sequences. ProGeRF was…

Extracts repetitive regions from genome and proteome sequences. ProGeRF was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse…

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STR-realigner
Desktop

STR-realigner

Proposes a dynamic programming based realignment method. STR-realigner…

Proposes a dynamic programming based realignment method. STR-realigner considers repeat patterns in short tandem repeat (STR) regions as prior knowledge. By allowing the size change of repeat…

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VNTRseek
Desktop

VNTRseek

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

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

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FDSTools
Desktop

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…

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HipSTR
Desktop

HipSTR Haplotype inference and phasing for Short Tandem Repeats

Allows genotyping, haplotyping, and phasing of short tandem repeats (STRs) from…

Allows genotyping, haplotyping, and phasing of short tandem repeats (STRs) from whole genome sequencing (WGS) data. HipSTR uses a multitude of inference techniques that integrate additional…

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MetaSV
Desktop

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…

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ATRHUNTER
Web

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.

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msatcommander
Desktop

msatcommander

Is designed to search for microsatellite arrays, design primers, and tag…

Is designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated,…

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SV-AUTOPILOT
Desktop

SV-AUTOPILOT Structural Variation AUTOmated PIpeLine Optimization Tool

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is…

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is a pipeline that can be used on existing computing infrastructure in the form of a Virtual Machine (VM) Image. It…

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SSR_pipeline
Desktop

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…

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STRait Razor
Desktop

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…

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TSSV
Desktop

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…

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PacmonSTR
Desktop

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.

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QDD
Web
Desktop

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.

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SHEAR
Desktop

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…

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iMSAT
Desktop

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.

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Geneious…
Desktop

Geneious Microsatellite Plugin

Allows to fit a ladder, call peaks, bin alleles and produce a table of…

Allows to fit a ladder, call peaks, bin alleles and produce a table of genotypes. Geneious Microsatellite Plugin allows to resolve problem with dirty data by manually adjusting curves, peaks, ladders…

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GMATo
Desktop

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.

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IMEx
Desktop
Web

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.

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AAARF
Desktop

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…

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SSRIT
Web
Desktop

SSRIT Simple Sequence Repeat Identification Tool

Researches all exact simple sequence repeats (SSRs) in a user sequence.

Researches all exact simple sequence repeats (SSRs) in a user sequence.

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SSR
Web

SSR Simple Sequence Repeats

Allows to count simple sequence repeats of different lengths in a DNA sequence.

Allows to count simple sequence repeats of different lengths in a DNA sequence.

RepeatMasker
Desktop
Web

RepeatMasker

Screens DNA sequences for interspersed repeats and low complexity DNA…

Screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a…

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detecttd
Desktop

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.

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MISA
Desktop

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.

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palfinder
Desktop

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.

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SSRLocator
Desktop

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.

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vcf2MSAT
Desktop

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.

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INVERTER
Desktop

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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