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…
Desktop app
G T A T C G C T A SAMtools SAMtools

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…

G T A T C G C T A Genome Analysis… Genome Analysis Toolkit-Queue

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…

Desktop app
G T A T C G C T A GATK UnifiedGenotyper GATK UnifiedGenotyper

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…

Desktop app
G T A T C G C T A BreakDancer BreakDancer

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…

Desktop app
G T A T C G C T A VarScan VarScan

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…

Desktop app
G T A T C G C T A MoDIL MoDIL

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.

Desktop app
G T A T C G C T A DeNovoGear DeNovoGear

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…

Desktop app
G T A T C G C T A SPLITREAD SPLITREAD

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.

Desktop app
G T A T C G C T A Dindel Dindel

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…

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 SOAPindel SOAPindel

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.

Desktop app
G T A T C G C T A Discovering Single… Discovering Single Nucleotide Polymorphism

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…

Desktop app
G T A T C G C T A Mendelian-inheritance-AtTEntive…

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…

Desktop app
G T A T C G C T A Structural Variant… Structural Variant Machine

SV-M Structural Variant Machine

Accurate indel prediction using paired-end short reads.

Accurate indel prediction using paired-end short reads.

Desktop app
G T A T C G C T A PyroHMMvar PyroHMMvar

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.

Desktop app
G T A T C G C T A HeurAA HeurAA

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.

Desktop app
G T A T C G C T A AgroMarker Finder AgroMarker Finder

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…

Desktop app
G T A T C G C T A Manta Manta

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…

Desktop app
G T A T C G C T A ReviSeq ReviSeq

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…

Desktop app
G T A T C G C T A GINDEL GINDEL

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…

Desktop app
G T A T C G C T A Universal Positioning… Universal Positioning System of indels

UPS-indel Universal Positioning System of indels

A tool that creates a universal positioning system for indels so that…

A tool that 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…

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 SomaticSeq SomaticSeq

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…

Desktop app
G T A T C G C T A FermiKit FermiKit

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…

Desktop app
G T A T C G C T A BreakSeek BreakSeek

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…

Desktop app
G T A T C G C T A indelMINER indelMINER

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…

Desktop app
Web app
G T A T C G C T A Vindel Vindel

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…

Desktop app
G T A T C G C T A Scalpel Scalpel

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…

Desktop app
G T A T C G C T A Assembly Based… Assembly Based ReAligner

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).

Desktop app
G T A T C G C T A Snippy Snippy

Snippy

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

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

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 Illuminator Illuminator

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.

Desktop app
G T A T C G C T A Syzygy Syzygy

Syzygy

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

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

Desktop app
G T A T C G C T A VARiD VARiD

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.

Desktop app
G T A T C G C T A piCALL piCALL

piCALL

Identifies short indel polymorphisms in population sequencing data.

Identifies short indel polymorphisms in population sequencing data.

Desktop app
G T A T C G C T A Indelocator Indelocator

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.

Desktop app
G T A T C G C T A FreeBayes FreeBayes

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.

Desktop app
G T A T C G C T A Strelka Strelka

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.

Desktop app
G T A T C G C T A Single Platform for… Single Platform for Analyzing Indels

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…

Desktop app
G T A T C G C T A VAAL VAAL

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%…

Desktop app
G T A T C G C T A SomaticIndelDetector Deprecated SomaticIndelDetector

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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