ngseasy: ngseasy-release-0.0.1

<p><strong>NGSeasy: A Dockerized NGS pipeline and tool-box</strong></p> <p>With NGSeasy you can now have full suite of NGS tools up and running on any high end workstation in an afternoon</p> <p>Release: ngseasy-release-0.0.1</p> <ul> <li>F1000 Research release</li> <li>Dockered Tool Version: 1.0-r001</li> <li>basic functionality :</li> <li>-- fastqc<br> -- trimmomatic<br> -- all aligners : bwa,bowtie2,snap,stampy,novoalign<br> -- var calling with freebayes or platypus</li> <li>indel realignment and BSQR : work in progress</li> <li>CNV Calling : work in progress</li> <li>Reports : work in progress</li> </ul> <p>We present <strong>NGSeasy (Easy Analysis of Next Generation Sequencing)</strong>, 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).</p> <p>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.).</p> <p>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.