This website uses cookies in order to improve our services. If you proceed visiting this website you accept the usage of cookies. For more info please read our Data Privacy statement.


NGS Software Tools - Complex Analysis Workflows

Complex Analysis Workflow | Quality Control & Data Trimming | Assembling & Binning | Alignment & Mapping | Data Analysis | Variant Analysis & Variant Calling | Data Bases & Data Base Search | Visualisation

  Cloud Services  | Workflow Management Software  | Analysis Workflows

Cloud Service

Amazon Elastic Compute Cloud (Amazon EC2)

Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides resizable compute capacity in the cloud. It is designed to make web-scale cloud computing easier for developers.
Source: Amazon web services



Azure supports the broadest selection of operating systems, programming languages, frameworks, tools, databases and devices. Run Linux containers with Docker integration; build apps with JavaScript, Python, .NET, PHP, Java and Node.js; build back-ends for iOS, Android and Windows devices.
Source: Microsoft Azure



Bramblecloud R clusters
Bramblecloud provides pre-configured cloud clusters to speed up R computations. The system is designed to work right out of the box, giving you additional computing power when you need it without the hassle of setting up the cloud infrastructure first. You can reliably integrate spot instances into your R cluster to save costs. There are special rates for university affiliates.


Illumina BaseSpace

BaseSpace is the Illumina cloud-based genomics hub for next-generation sequencing (NGS) data management and analysis. Sequencing labs can securely store and share sequencing data, and researchers can simplify and accelerate NGS data analysis with push-button tools. Labs can also set-up and monitor their sequencing runs in real time on any Illumina instrument. BaseSpace can be accessed via an intuitive web-based interface or Linux-based command line tool.

Source: Illumina


The goal of Magellan, a project funded through the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR), was to investigate the potential role of cloud computing in addressing the computing needs for the DOE Office of Science (SC), particularly related to serving the needs of mid- range computing and future data-intensive computing workloads.
Source: Argonne National Laboratory


Thermo Fisher Cloud

Thermo Fisher Cloud provides scientists with a secure place to store, analyze, and share data. Upload data from one of our cloud-connected instruments or upload your own files from anywhere you have web access. With the Cloud Connect Utility, you can upload files by simply placing them in a folder on your computer that is synced to the Cloud. Use one of our cloud-based apps to analyze your data with the power of cloud computing, then share the results with your colleagues to observe patterns, validate findings, and develop insights. And it's not just for data files. Upload your presentation for that upcoming conference or a great how-to video you created and want colleagues to see.

Source: Thermo Fisher

Workflow Management Software


Chipster is a user-friendly analysis software for high-throughput data. It contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
Source: Chipster



GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.
Source: Broad Institute



The Kepler software helps users share and reuse data, workflows, and compo¬nents developed by the scientific community to address common needs.
Source: Kepler



KNIME is the leading open platform for data-driven innovation helping organizations to stay ahead of change. Innovative organizations use our open-source, enterprise-grade analytics platform to discover the potential hidden in their data, mine for fresh insights, or predict new futures.
Source: Knime


Pipeline Pilot

Pipeline Pilot enables scientists to rapidly create, test and publish scientific services that automate the process of accessing, analyzing and reporting scientific data, either for the scientist’s personal use or for sharing across the scientific community.
Source: BIOVIA



Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and executescientific workflows and aid in silico experimentation.
Source: Taverna


Analysis Workflow

Illumina’s Analysis Visual Controller software v1.7 (AVC)

Illumina’s Analysis Visual Controller software v1.7 (AVC) provides a graphical user interface to perform a complete offline data analysis of a sequencing run. In the usual workflow, Real Time Analysis (RTA) will perform the image processing and base calling during the sequencing run. AVC will then be used to run CASAVA for alignment and variant detection (secondary analysis). AVC also supports image analysis, base calling, or alignment using the Offline Linux Basecaller (OLB) or the older analysis software Pipeline. In addition, AVC supports demultiplexing.
Source: Illumina



BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.



Bedtools a powerful toolset for genome arithmetic, it allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Source: Bedtools



Biobase offers different human genome analysis tools.


Bina Genomic Management Solutions


Bioconductor software

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.


BaseSpace Isaac Enrichment and Isaac Whole Genome Sequencing

CASAVA, As a replacement for CASAVA, we have added functionality to the BaseSpace Isaac Enrichment and Isaac Whole Genome Sequencing apps available on BaseSpace and BaseSpace Onsite. In addition, the bcl2fastq Conversion Software is available to demultiplex and convert BCL files to FASTQ files on your local computer hardware.


CLCBio Genetic workbench

CLCBio Genetic workbench A comprehensive and user-friendly analysis package for analyzing, comparing, and visualizing next generation sequencing data.
Source: Qiagen



Galaxy web based analysis workflow



This software is a powerful complete analysis workflow. It offers a wide range of applications starting from assembly, alignment, variant calling and different analysis.


GO Clinical Workbench

The GO Clinical Workbench provides a single workflow that starts with NGS data files (VCF and BAM) from the sequencer through a step-by-step process to create a clinical report. Focus is on clinical oncology.



GenomePilot™ enables anyone—from bioinformaticians to researchers to technicians—to define and execute complex analyses without any sophisticated IT experience. A user-friendly interface organizes tools, data, and processes and provides context-sensitive prompts to guide users in selecting parameters or creating new processes.



GensearchNGS is an integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina, Ion Torrent and Proton. It integrates all the steps from importing and filtering sequence reads, bar code splitting, alignment, variant detection and annotation to the final report of detected variants. Variants can be annotated with various public and private data sources (Ensembl, Alamut, Genome Trax,...) They can be filtered by logical combinations between samples for family studies.

Source: Phenosystems



GNATY, short for GensearchNGS Analysis Tools librarY, is a collection of stand alone tools developed for GensearchNGS, a user friendly NGS data analysis software suite developed by Phenosystems SA. The main goal of GNATY is to provide user friendly tools for NGS data analysis that are fast and efficient, thus reducing the overall time for NGS data analysis.
Source: GNATY



khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis.
Source: khmer


Lab7 Enterprise Science Platform (ESP)

The Lab7 Enterprise Science Platform (ESP) is the first complete sample-to-answer software platform for Next Generation Sequencing. By combining LIMS features with an advanced analysis pipeline manager and reporting framework, the Lab7 ESP enables you to manage your entire sequencing workflow. The heart of the Lab7 ESP is a fully customizable workflow engine that organizes your lab around different sequencing workflows. Lab7 Workflows encompass not only wet lab operations but support full integration of analysis and reporting, drastically reducing the amount of IT "machinery" required to manage, process, and analyze samples.
Source: lab7


Lasergene Genomics Suite

Laserergene Genomic Suite DNAstar complete worklfow keeps it simple, providing all the software you need for next-gen sequence assembly and analysis, in a single integrated package. We support all major NGS technologies, making it easy to work with your data for any type of NGS project.
Source: DNAstar


MiSeq Reporter analysis software

The MiSeq Reporter analysis software processes base calls generated on-instrument during the sequencing run by Real Time Analysis (RTA) software, and produces information about alignment, structural variants, and contig assemblies for each genome requested and each sample based on the analysis workflow specified in the sample sheet.
Source: Illumina



NextGENe is the perfect analytical partner for the analysis of desktop sequencing data produced by the ION PGM™, Roche Junior, Illumina MiSeq as well as high throughput systems as the Ion Torrent Proton, Roche FLX, Applied BioSystems SOLiD™ and Illumina® platforms. NextGENe software runs on a Windows® Operating System, which provides a biologist-friendly point & click interface, and does not require scripting or other bioinformatics support.
Source: Softgenetics


OmicsOffice for NGS (SeqSolve)

OmicsOffice for NGS (SeqSolve) is an advanced and user-friendly software solution for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.
Powered by OmicsOffice and by integrating state-of-the-art bioinformatics methods into one-click analysis workflows, SeqSolve is the only software able to provide scientists with such a combination of both cutting edge and intuitive user experience. Its Click And Go® technology enables the automatic processing of the data, which makes it simple to use for non-experts, along with a smart quality control system to prevent experimental biases. SeqSolve results are therefore consistent, biologically relevant and reliable.
Source: Integromics


Partek Workflow

Partek provides a start-to-finish data analysis software solution for next generation sequencing applications including DNA, Transcriptome, and Gene Regulation. Take advantage of our pre-installed analysis pipelines and workflows to perform analysis without ever typing a single line of code.
Source: Partek



Sequencher brings some of the best peer-reviewed NGS algorithms out of the command line and into your hands. Beginners can start aligning their NGS data immediately while advanced users still have access to each command line input via an easy to understand interface. Perform SNP analyses, align methylated data, and perform de novo assemblies or reference-guided alignments. Sequencher's latest NGS functionality includes RNA-Seq data analysis with the addition of the Cufflinks suite.
Source: Genecodes


Strandngs (Formerly Avadis NGS)

Strandngs (Formerly Avadis NGS) is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, Methyl-Seq, MeDIP-Seq, and ChIP-Seq experiments.
Source: Stand-NGS



TimeLogic, the bioinformatics brand of Active Motif, provides high-performance Biocomputing systems that combine custom designed Field Programmable Gate Array (FPGA) circuitry with optimized implementations of fundamental bioinformatics algorithms.
Source: TimeLogic



USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at the Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.
Source: Sourceforge


Pin It