What is EDGE?
EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.
While the design of EDGE was intentionally done to be as simple as possible for the user, there is still no single ‘tool’ or algorithm that fits all use-cases in the bioinformatics field. Our intent is to provide a detailed panoramic view of your sample from various analytical standpoints, but users are encouraged to have some insight into how each tool or workflow functions, and how the results should best be interpreted.
We have two image/container type of EDGE development version implementations. We would recommend to use Docker container for easy update in the future.
- Development Docker image is public. See DOCKER HUB.
- EDGE development version Virtual Machine Image
- A demonstration version of EDGE has been updated to development versions at https://bioedge.lanl.gov/.
- Change Log
- [nature.com] How bioinformatics tools are bringing genetic analysis to the masses
- [genomeweb.com] LANL's EDGE Offers Easy-to-Use Bioinformatics Pipelines for Microbial Sequence Analysis
- [santafenewmexican.com] Science on the Hill-Bringing the power of genetic research to an office near you
- EDGE version v1.5.1 pre-release.
- NCBI is moving from http to https for security and privacy improvement which caused SRA download feature failed. We have updated our script to accommondate the change. In addition, if it failed to download from NCBI-SRA, it will try EBI-ENA and DDBJ.
- One of the MetaComp requirements udpated its version (cowplot) broken the EDGE installation: update R version from 3.2.2 to 3.3.2 and MetaComp from v1.1 to v1.2
- EDGE manuscript has been published on Nucleic Acids Research (2016). See Abstract.
- EDGE news on eurekalert.org
- EDGE version v1.5.0 release.
- The EDGE documentation has branches with version v1.5 and develop for development (active updating)
- EDGE development branch on GitHub. and its Poster
- The EDGE documentation has branches with version v1.1 and develop for development (active updating)
- fix bugs: batch submit point to wrong path. Escape symbol characters.
- fix bug: run the EDGE through command line with absoulte path.
- remove unsupport taxanomy profiling tool in the example config file
- make the example apache configuration file ready for copy with EDGE installation script
- A preprint manuscript is on bioRxiv.
- Version 1.1 source code released
- Have Docker image ready. See DOCKER HUB
- Databases can be downloaded through FTP server
A demonstration version of EDGE is currently available at https://bioedge.lanl.gov/ with example data sets available to the public to view and/or re-run and also allows EDGE runs of SRA/ENA data. (This webserver does not currently support upload of data due in part to LANL security regulations, however local installations are meant to be fully functional.) To run EDGE, go to the EDGE webpage. You will need to create an account in order to start a project, which you can do with the icon in the top right corner. Once you've created an account and have logged in, you can start a project. From the menu on the left, click "Run EDGE". This will open a page titled "Input your sample", and from here you will see a list of drop down menus that will allow you to label your project, input FASTQ files, and select the tools you would like to use. Pre-Processing, Assembly and Annotation, and Taxonomy Classification are turned on by default. While your project is running you can watch it's progress and system usage using the Job Progress sidebar, which opens using the icon in the top right corner. For those that want to run EDGE v1.1 offline, installation instructions can be found in our documentation, which can be accessed https://edge.readthedocs.io/en/v1.1/index.html. There is also a link to the documentation on the EDGE website. For basic information about EDGE, visit the EDGE ABC’s, that provide a brief overview of EDGE, the various workflows, and the computational environment restraints for local use.
Once your project is completed, EDGE will create an output report that contains a brief summary of the run, along with a list of drop down menus that show the EDGE tools used and detailed reports. The final data is listed in these menus and visualized through a tool called Krona, an interactive browser that allows the exploration of hierarchical data with pie charts. You can also see the full data by downloading the report PDF's, found at the bottom of each output section.
Discussions / Bugs Reporting
We have created a mailing list for EDGE users. If you would like to recieve notifications about the updates and join the discussion, please join the mailing list by becoming the member of edge-users groups.
We appreciate any feedback or concerns you may have about EDGE. If you encounter any bugs, you can report them to our GitHub issue tracker.
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform Po-E Li; Chien-Chi Lo; Joseph J. Anderson; Karen W. Davenport; Kimberly A. Bishop-Lilly; Yan Xu; Sanaa Ahmed; Shihai Feng; Vishwesh P. Mokashi; Patrick S.G. Chain Nucleic Acids Research 2016; Publicationdoi: 10.1093/nar/gkw1027
Los Alamos National Security, LLC (LANS) owns the copyright to EDGE, which it identifies internally as LA-CC-14-007. The license is GPLv3. See LICENSE for the full text.