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NGSeasy ==================== ** This is the latest dev project ** [Funded by Biomedical Research Centre](http://core.brc.iop.kcl.ac.uk): http://core.brc.iop.kcl.ac.uk Publication: pending Authors: Stephen J Newhouse, Amos Folarin , Maximilian Kerz Release Version: **1.0.0b** **************** ### [A [Dockerized](https://www.docker.com/) NGS pipeline and tool-box] **************** **With NGSeasy you can now have full suite of NGS tools up and running on any high end workstation in an afternoon** **Getting started: [The 12 Easy Steps to NGS Freedom!](https://github.com/KHP-Informatics/ngs#the-12-easy-steps-to-ngs-freedom)** **Note:** NGSeasy is under **heavy development** and the code and docs evolve quickly. - **NGSeasy-v1.0 Full Production release will be available Early 2015** - **NGSeasy-v1.0.0b Full Production release contains most of the core fucntionality to go from raw fastq to raw vcf calls** - **NGSeasy updates every 12 months** - **GUI in development** - **Contact us of Reference Genomes and resource files** **************** >NGSeasy is completely open source and we encourage interested folks to jump in and get involved in the dev with us. **************** NGSeasy (Easy Analysis of Next Generation Sequencing) ======================================================= We present **NGSeasy (Easy Analysis of Next Generation Sequencing)**, a flexible and easy-to-use NGS pipeline for automated alignment, quality control, variant calling and annotation. The pipeline allows users with minimal computational/bioinformatic skills to set up and run an NGS analysis on their own samples, in less than an afternoon, on any operating system (Windows, iOS or Linux) or infrastructure (workstation, cluster or cloud). NGS pipelines typically utilize a large and varied range of software components and incur a substantial configuration burden during deployment which limits their portability to different computational environments. NGSeasy simplifies this by providing the pipeline components encapsulated in Docker™ containers and bundles in a wide choice of tools for each module. Each module of the pipeline represents one functional grouping of tools (e.g. sequence alignment, variant calling etc.). Deploying the pipeline is as simple as pulling the container images from the public repository into any host running Docker. NGSeasy can be deployed on any medium to high-end workstation, high performance computer cluster and compute clouds (public/private cloud computing) - enabling instant access to elastic scalability without investment overheads for additional compute hardware and makes open and reproducible research straight forward for the greater scientific community. ### Advantages ### - Easy to use for non-informaticians. - All run from a single config file that can be made in Excel. - User can select from mutiple aligners, variant callers and variant annotators - No scary python, .yaml or .json files...just one simple Excel workbook saved as a textfile. - Just follow our simple set of instructions and NGS away! - Choice of aligners and variant callers and anntators - Allows reproducible research - Version controlled for auditing - Customisable - Easy to add new tools - If it's broke...we will fix it.. - Enforced naming convention and directory structures - Allows users to run "Bake Offs" between tools with ease We have adapted the current best practices from the Genome Analysis Toolkit (GATK, http://www.broadinstitute.org/gatk/guide/best-practices) for processing raw alignments in SAM/BAM format and variant calling. The current workflow, has been optimised for Illumina platforms, but can easily be adapted for other sequencing platforms, with minimal effort. As the containers themselves can be run as executables with pre-specified cpu and RAM resources, the orchestration of the pipeline can be placed under the control of conventional load balancers if this mode is required. **** ### Author Contact Details Please contact us for help/guidance on using the beta release. - Amos Folarin <amosfolarin@gmail.com> [@amosfolarin](https://twitter.com/amosfolarin?lang=en) <a href="http://www.linkedin.com/pub/amos-folarin/34/b06/978"> <img src="http://www.linkedin.com/img/webpromo/btn_viewmy_160x33.png" width="160" height="33" alt="View Amos's profile on LinkedIn"> </a> - Stephen J Newhouse <stephen.j.newhouse@gmail.com> [@s_j_newhouse](https://twitter.com/s_j_newhouse?lang=en) <a href="http://uk.linkedin.com/pub/dr-stephen-newhouse/29/89a/11a"> <img src="http://www.linkedin.com/img/webpromo/btn_viewmy_160x33.png" width="160" height="33" alt="View Steve's profile on LinkedIn"> </a> **Lets us know if you want other tools added to NGSeasy** *Institution: NIHR Maudsley Biomedical Research Centre For Mental Health and Dementia Unit (Denmark Hill), at The Institute of Psychiatry, Psychology & Neuroscience (IoPPN), Kings College London* ****************