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Indel detection software tools | High-throughput sequencing data analysis

Insertion and deletion (indel) mutations, the most common type of structural variance in the human genome, affect a multitude of human traits and diseases. New sequencing technologies, such as deep sequencing, allow massive throughput of sequence…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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SMRT-SV
Desktop

SMRT-SV

Allows to identify missing sequence and genetic variation. SMRT-SV generates…

Allows to identify missing sequence and genetic variation. SMRT-SV generates data about DNA sequences. The distinctive feature of this tool is that native DNA is sequenced without cloning or…

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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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GATK…
Desktop

GATK UnifiedGenotyper

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian…

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype likelihood model to estimate simultaneously the most likely genotypes and allele frequency in a population of N…

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Syzygy
Desktop

Syzygy

SNP and indel calling for pooled and individual targeted resequencing studies.

SNP and indel calling for pooled and individual targeted resequencing studies.

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BreakDancer
Desktop

BreakDancer

A Perl/C++ package that provides genome-wide detection of structural variants…

A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10…

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DeNovoGear
Desktop

DeNovoGear

A software tool for analyzing de novo mutations from familial and somatic…

A software tool for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation…

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MoDIL
Desktop

MoDIL

A novel method for finding medium sized indels from high throughput sequencing…

A novel method for finding medium sized indels from high throughput sequencing datasets.

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VarScan
Desktop

VarScan

A platform-independent mutation caller for targeted, exome, and whole-genome…

A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan…

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SPLITREAD
Desktop

SPLITREAD

A method for detecting INDELs (small insertions and deletion with size less…

A method for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions deletions that are within the coding regions from the exome sequencing data.

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VAAL
Desktop

VAAL

A package to use massively parallel DNA sequence data to identify differences…

A package to use massively parallel DNA sequence data to identify differences between bacterial genomes at high sensitivity and specificity. VAAL is a variant ascertainment algorithm which found ~98%…

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Nanopolish
Desktop

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov…

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format…

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Scalpel
Desktop

Scalpel

A software package for detecting INDELs (INsertions and DELetions) mutations in…

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). Scalpel is…

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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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Pyrotools
Desktop

Pyrotools

Represents the consensus sequences in a region of interest (ROI). Pyrotools is…

Represents the consensus sequences in a region of interest (ROI). Pyrotools is based on the graph technique that resembles the partial order graph or variant graph. It can model error patterns in the…

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Dindel
Desktop

Dindel

A Bayesian method to call indels from short-read sequence data in individuals…

A Bayesian method to call indels from short-read sequence data in individuals and populations by realigning reads to candidate haplotypes that represent alternative sequence to the reference. The…

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MATE-CLEVER
Desktop

MATE-CLEVER Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder

An approach that accurately discovers and genotypes indels longer than 30 bp…

An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or…

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discoSnp++
Desktop

discoSnp++ Discovering Single Nucleotide Polymorphism

Detects both heterozygous and homozygous isolated SNPs from any number of read…

Detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed…

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SOAPindel
Desktop

SOAPindel

Focusing on calling indels from the next-generation paired-end sequencing data.

Focusing on calling indels from the next-generation paired-end sequencing data.

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Strelka
Desktop

Strelka

A method for somatic SNV and small indel detection from sequencing data of…

A method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples.

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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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AMF
Desktop

AMF AgroMarker Finder

A GUI software for providing graphical user interface (GUI) to facilitate the…

A GUI software for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. AMF integrates sophisticated…

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SomaticSeq
Desktop

SomaticSeq

An accurate somatic mutation detection pipeline implementing a stochastic…

An accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions…

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INDELseek
Desktop

INDELseek

Detects complex indels from next-generation sequencing (NGS) reads. INDELseek…

Detects complex indels from next-generation sequencing (NGS) reads. INDELseek was demonstrated as an accurate and versatile complex indel caller, which is compatible with somatic and germline…

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BreakSeek
Desktop

BreakSeek

A breakpoint-based algorithm, which can unbiasedly and efficiently detect both…

A breakpoint-based algorithm, which can unbiasedly and efficiently detect both homozygous and heterozygous INDELs, ranging from several base pairs to over thousands of base pairs, with accurate…

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Manta
Desktop

Manta

Calls structural variants (SVs) and indels from mapped paired-end sequencing…

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and…

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VarCap
Desktop

VarCap

Allows to reliably identify variants. VarCap is a workflow for accurate and…

Allows to reliably identify variants. VarCap is a workflow for accurate and sensitive genotyping of prokaryotic populations. It permits scientists to rapidly predict variants within high coverage,…

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piCALL
Desktop

piCALL

Allows population indel detection and genotyping. piCALL detects and allows…

Allows population indel detection and genotyping. piCALL detects and allows genotyping of small indels from population-scale sequence data. The software is compatible with data from different…

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VARiD
Desktop

VARiD

A Hidden Markov Model for SNP and indel identification with AB-SOLiD…

A Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads.

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PyroHMMvar
Desktop

PyroHMMvar

Calls single nucleotide polymorphisms (SNPs) and short indels for both Ion…

Calls single nucleotide polymorphisms (SNPs) and short indels for both Ion Torrent and 454 resequencing data. PyroHMMvar is a method that has two distinct features: (i) an HMM to formulate…

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SPAI
Desktop

SPAI Single Platform for Analyzing Indels

An interactive platform for analyzing indels. SPAI facilitates users to run…

An interactive platform for analyzing indels. SPAI facilitates users to run several popular indel calling tools and perform several analyses on the indel calling results without knowing any command…

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SV-M
Desktop

SV-M Structural Variant Machine

Detects indel candidates using a discriminative classifier based on features of…

Detects indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing.…

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GVC
Desktop

GVC Genomic Variant Caller

Detects various genomic variants including single nucleotide variant (SNV),…

Detects various genomic variants including single nucleotide variant (SNV), single insertion/deletion (sINDEL) and structural variation (SV) from personal and normal-cancer paired whole-genome/exome…

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TSNAD
Desktop

TSNAD

Identifies cancer somatic mutations following the best practices of the genome…

Identifies cancer somatic mutations following the best practices of the genome analysis toolkit (GATK) from the genome/exome sequencing data of tumor-normal pairs. TSNAD is an integrated software…

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16GT
Desktop

16GT

Provides a variant caller for Illumina whole genome sequencing (WGS) and whole…

Provides a variant caller for Illumina whole genome sequencing (WGS) and whole exome sequencing (WES) germline data. 16GT uses a new 16-genotype probabilistic model to unify single nucleotide…

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SvABA
Desktop

SvABA Structural variation and indel Analysis By Assembly

Detects structural variants (SVs) from short-read sequencing data using…

Detects structural variants (SVs) from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. SvABA’s performance was evaluated on the NA12878 human…

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UPS-indel
Desktop
Web

UPS-indel Universal Positioning System of indels

Creates a universal positioning system for insertions/deletions (indels) and…

Creates a universal positioning system for insertions/deletions (indels) and allows to compare indel calling results produced by different tools. UPS-indel is a universal positioning system for…

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FermiKit
Desktop

FermiKit

A variant calling pipeline for Illumina whole-genome germline data. It de novo…

A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions…

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ScanIndel
Desktop

ScanIndel

Detects indels with multiple heuristics including gapped alignment, split reads…

Detects indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, it was demonstrated ScanIndel’s superior sensitivity and specificity…

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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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Illuminator
Desktop

Illuminator

A sequence alignment program for the output from Illumina GA-II clonal…

A sequence alignment program for the output from Illumina GA-II clonal sequencers.

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indelMINER
Desktop

indelMINER

A set of algorithms and heuristics to identify indels from whole genome…

A set of algorithms and heuristics to identify indels from whole genome resequencing datasets using paired-end reads. indelMINER uses a split-read approach to identify the precise breakpoints for…

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GINDEL
Desktop

GINDEL

An approach for calling genotypes of both insertions and deletions from…

An approach for calling genotypes of both insertions and deletions from sequence reads. GINDEL uses a machine learning approach which combines multiple features extracted from next generation…

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BBCAnalyzer
Desktop

BBCAnalyzer

Allows the visualization of the relative or absolute number of bases, deletions…

Allows the visualization of the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference…

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ShiftDetector
Web

ShiftDetector

Scans a trace file for such a shift, and predicts the sequence of the DNA…

Scans a trace file for such a shift, and predicts the sequence of the DNA molecule following the site of the shift. ShiftDetector analyses a sequencing trace file in order to discover if it is a…

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Vindel
Desktop
Web

Vindel

Detects redundant indels. Vindel, a simple yet effective computational…

Detects redundant indels. Vindel, a simple yet effective computational pipeline, can be used to check whether a set of indels are redundant with respect to those already in the database of interest…

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HeurAA
Desktop

HeurAA

Accurate and fast detection of genetic variations with a novel heuristic…

Accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK is composed of several tools…

Focuses on variant discovery and genotyping. GATK is composed of several tools and is able to support projects of any size. This tool is a collection of command line for the analyse of…

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ReviSeq
Desktop

ReviSeq

Revises a genome sequence of a prokaryotic sample. ReviSeq uses a hybrid method…

Revises a genome sequence of a prokaryotic sample. ReviSeq uses a hybrid method comprised of iterative remapping and local assembly upon a bacterial sequence backbone. This method was applied to six…

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Cassiopee-c
Desktop

Cassiopee-c

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find…

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find exact match and allows substitutions, insertions and deletions. It can make indexation based on a suffix tree with…

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Snippy
Desktop

Snippy

Find SNPs/indels in a bacterial genome from NGS reads.

Find SNPs/indels in a bacterial genome from NGS reads.

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Indelocator
Desktop

Indelocator

A software tool for calling short indels in next generation sequencing data.

A software tool for calling short indels in next generation sequencing data.

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FreeBayes
Desktop

FreeBayes

A Bayesian genetic variant detector designed to find small polymorphisms,…

A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

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LifeScope
Desktop

LifeScope

Leverages years of customer feedback and development for analysis tools for…

Leverages years of customer feedback and development for analysis tools for SOLiD system data, to enable faster translation of next-generation data to biologically meaningful results. Designed to…

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SomaticIndelDet…
Desktop

SomaticIndelDetector

The Somatic Indel Detector can be run in two modes: single sample and paired…

The Somatic Indel Detector can be run in two modes: single sample and paired sample. In the former mode, exactly one input bam file should be given, and indels in that sample are called. In the…

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