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 data and greatly contribute to…
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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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GATK-Queue
Cloud

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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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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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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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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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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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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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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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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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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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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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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SV-M
Desktop

SV-M Structural Variant Machine

Accurate indel prediction using paired-end short reads.

Accurate indel prediction using paired-end short reads.

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PyroHMMvar
Desktop

PyroHMMvar

A program to call short indels and SNPs for Ion Torrent and 454 data.

A program to call short indels and SNPs for Ion Torrent and 454 data.

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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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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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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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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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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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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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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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UPS-indel
Desktop

UPS-indel Universal Positioning System of indels

Creates a universal positioning system for indels so that equivalent indels can…

Creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system. UPS-indel can be used to compare indels to see whether…

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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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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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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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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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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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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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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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ABRA
Desktop

ABRA Assembly Based ReAligner

It uses localized assembly and global realignment to align reads more…

It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

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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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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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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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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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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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piCALL
Desktop

piCALL

Identifies short indel polymorphisms in population sequencing data.

Identifies short indel polymorphisms in population sequencing data.

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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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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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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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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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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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