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Workflow/pipeline software tools | Whole-exome sequencing data analysis

These pipeline and workflow tools provide out-of-the box solutions for whole-exome sequencing analysis by chaining a number of specific analysis tools together.

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RUbioSeq
Desktop

RUbioSeq

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq…

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq,…

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SIMPLEX
Server

SIMPLEX

Allows to obtain biological insight into genetic events investigated by exome…

Allows to obtain biological insight into genetic events investigated by exome sequencing. Simplex is an automatized pipeline for investigating exome single-end (SE) and paired-end (PE) sequencing…

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MutAid
Desktop

MutAid

A pipeline to analyze and interpret raw sequencing data produced by Sanger or…

A pipeline to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. MutAid performs format conversion, base calling, quality trimming, filtering, read…

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Cpipe
Desktop

Cpipe

A variant detection pipeline designed to process high throughput sequencing…

A variant detection pipeline designed to process high throughput sequencing data, with the purpose of identifying potentially pathogenic mutations. Cpipe offers an industry standard variant calling…

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GotCloud
Desktop

GotCloud Genomes on the Cloud

A pipeline for efficiently detecting and genotyping high-quality variants from…

A pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling,…

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OpEx
Desktop

OpEx Optimised Exome

Comprises a fixed implementation of alignment, calling and annotation tools…

Comprises a fixed implementation of alignment, calling and annotation tools optimised for individual/multiple exome sequencing analysis in the clinical setting or the research. OpEx is customizable…

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IMPACT
Desktop

IMPACT Integrating Molecular Profiles with ACtionable Therapeutics

A whole exome sequencing (WES) data analysis pipeline that integrates both…

A whole exome sequencing (WES) data analysis pipeline that integrates both single nucleotide variants and copy number alterations from WES data to identify a list of candidate genes for therapeutic…

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OTP
Web

OTP One Touch Pipeline

Provides a platform for storing, handling and processing next generation…

Provides a platform for storing, handling and processing next generation sequencing (NGS) data. OTP performs both data management and processing and allows users to automate an entire process to raw…

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WEP
Web

WEP

Performs a complete whole-exome sequencing pipeline and provides easy access…

Performs a complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results. A user can perform the whole analysis without knowing the underlying…

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NGS-pipe
Desktop

NGS-pipe

Allows to develop tailored workflows for the analysis of whole-exome (WES),…

Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of…

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Fastq2vcf
Desktop

Fastq2vcf

An integrated analysis pipeline for whole-exome sequencing (WES) data analysis.…

An integrated analysis pipeline for whole-exome sequencing (WES) data analysis. Fastq2vcf offers improved flexibility, efficiency, and reproducibility. It can generate shell scripts that automate the…

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MitoSeek
Desktop

MitoSeek

An open-source software tool that can reliably and easily extract mitochondrial…

An open-source software tool that can reliably and easily extract mitochondrial genome information from exome and whole genome sequencing data. MitoSeek evaluates mitochondrial genome alignment…

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EthSEQ
Desktop

EthSEQ

An R script that allows to infer ethnicity of a set of samples for which whole…

An R script that allows to infer ethnicity of a set of samples for which whole exome sequencing (WES) data is available from differential SNP genotypes profiles. EthSEQ combines the 1,000 Genomes…

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TIGEM Exome…
Desktop

TIGEM Exome Mendelian Disorder Pipeline

Automates the analysis workflow (quality control and read trimming, mapping on…

Automates the analysis workflow (quality control and read trimming, mapping on reference genome, post-alignment processing, variation calling and annotation) using state-of-the-art software tools.

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WES
Desktop

WES Whole Exome Sequencing Analysis Pipeline

Processes next-generation sequencing (NGS) data through a semi-automated…

Processes next-generation sequencing (NGS) data through a semi-automated pipeline. WES encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. It uses a…

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STORMSeq
Desktop

STORMSeq Scalable Tools for Open-Source Read Mapping

A graphical interface cloud computing solution that does not require a parallel…

A graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping,…

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TREVA
Desktop

TREVA Targeted REsequencing Virtual Appliance

Support a series of analyses commonly required for targeted resequencing and…

Support a series of analyses commonly required for targeted resequencing and whole exome sequencing data, including: single-nucleotide and insertion/deletion variant calling, copy number analysis,…

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SeqMule
Desktop

SeqMule

A computational pipeline to perform automated variant calling from NGS data on…

A computational pipeline to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the…

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Omixon Target…
Desktop

Omixon Target Data Analysis

Application suite developed with a vision of helping clinical labs to adopt…

Application suite developed with a vision of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets.

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SeqBench
Server

SeqBench

Supports the management and analysis of exome sequencing data. SeqBench…

Supports the management and analysis of exome sequencing data. SeqBench combines data management, data analysis, and result visualization into a single web-based platform. The software is a web-based…

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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