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COVID19
COVID-19 Genome Analytics
A platform for COVID-19 analytics
New to EDGE
2.0.0
New to EDGE?
edge main workflow
2.4.1
Run EDGE
EDGE bioinformatics
edge qiime workflow
2023.5
Run QIIME2
Amplicon Data Analysis, 16s, 18s, and Fungal ITS
edge piret workflow
0.3.2 beta
Run PiReT
A pipeline for Reference based Transcriptomics analysis.
edge phame workflow
1.0.0
Run PhaME
Phylogenetic and Molecular Evolution (PhaME) analysis tool.
edge nanopore
Nano-EDGE
Run EDGE for Nanopore dataset.
edge contig
contig-EDGE
Run EDGE for assembled contig fasta files.
edge sra
sra-EDGE
Run EDGE for Sequence Read Archive
edge report workflow
1.0.0
Reports
Create summary tables for multiple projects.
edge project list
1.0.0
Project List
edge upload
1.0.0
Upload Data
Allowed File types are fastq, fasta, genbank, gff, hmm, xlsx and text (txt,bed,config,ini) and can be in gzip format.

Empowering the Development of Genomics Expertise

EDGE bioinformatics is intended to help truly democratize the use of Next Generation Sequencing for exploring genomes and metagenomes. Given that bioinformatic analysis is now the rate limiting factor in genomics, we developed EDGE bioinformatics with a user-friendly interface that allows scientists to perform a number of tailored analyses using many cutting-edge tools. A complete version of EDGE is available as a variety of packages that can fit individual needs, including source code, or images in VMware and Docker formats. For basic information about EDGE, visit the EDGE ABCs, that provide a brief overview of EDGE, the various workflows, and the computational environment restraints for local use.

EDGE Workflow

EDGE_sWorkflow EDGE_workflow

Features of EDGE

Implementation

Download & Updates

Source code: LANL-Bioinformatics GitHub site.
VM image: location and instructions.
Docker image: location and instructions.

Please visit EDGE Homepage for latest news and updates.

Tutorial & Help

The EDGE tutorial video series is hosted in Youtube. The detailed documentation and guide are hosted in edge.readthedocs.io in (click here for PDF version). User discussion group can be found here.

Publication

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 (2016), Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Nucleic Acids Research (doi: 10.1093/nar/gkw1027)

Input Your Sample

EDGE requires FASTQ sequence data files in FASTQ format or Contigs sequence data file in FASTA format. EDGE allows both paired-end and single-end sequences.

The Qiime2 pipeline requires sequence data files in FASTQ format and a mapping file. The sequence file is either paired-end or single-end sequences.Or directory with demultiplexed fastq files. Please see the documentation for more information.

The DETEQT is a pipeline for diagnostic targeted sequencing adjudication. Please see the documentation for more information.

The PiReT is a pipeline for Reference based Transcriptomics analysis. Please see the documentation for more information.

Input Raw Reads

Amplicon Type
Input Source
Platform

(Internet required) Input SRA accessions (comma separate for > 1 input) support studies (SRP*/ERP*/DRP*), experiments (SRX*/ERX*/DRX*), samples (SRS*/ERS*/DRS*), runs (SRR*/ERR*/DRR*), or submissions (SRA*/ERA*/DRA*). ex: SRR11241255

file
Reads Type

Sequencing Reads:

file
file Delete

and/or

file Delete
Dir
file Delete
file
| additional options |
Add Paired-end Input Add Single-end Input Add Mapping File Field
file

Your customized parameters can be used again. You can utilize the file selector above to upload a standard config file generated by EDGE bioinformatics.

Batch Project Submission

Run EDGE with Multiple projects using a tools set configuration. Click Download [Sample File] to see the example.

file

Input Metadata

Study


Sample
Sample Type
Host Condition

Recent Travels

Add a travel


Symptoms

(please check all that apply):



Experiment


OtherLearn more

Enter your own metadata as:
field1=value1
field2=value2
field3=value3
...



Choose Processes / Analyses

EDGE provides many modules to do various analyses. You can choose to run or skip a specific process. Parameters/options are provided for most of the analyses. You can click here to turn all on, expand all sections or close all sections.

Quality Trim and Filter
Stitch Paired-End Reads
Host Removal
Run Quality Trim and Filter
Quality Offset
Primer Trim Method
file
file
Remove Adapter by Porechop
Trim polyA
Run Stitch PE Reads
Use joined PE reads only
Run Host Removal

and/or

file

Assembly
Annotation
Binning
Bypass Assembly And Use Pre-assembled Contigs
file
Assembler

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimise. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

Bridging mode
file

LRASM is designed for long noise reads such as reads from Nanopore and it assemble fastq/fasta formatted reads using miniasm/wtdbg2/flye and use racon to perform consensus.

Algorithm
Error Correction
Preset

IDBA_UD performs well on isolates as well as metagenomes but it may not work well on very large genomes.

SPAdes performs well on isolates as well as single cell data but it may not work on larger genomes, and it takes more computational resource. PacBio CLR and Oxford Nanopore reads are used for gap closure and repeat resolution.

file
file

MEGAHIT is an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph which achieves low memory assembly.

Validation Aligner
| additional options |
Extract Unmapped/Unassembled Reads
Annotation
Annotation Tool
Specify Kingdom
KEGG Pathway View
file
Secondary Metabolite Analysis

Secondary Metabolite Analysis Parameters

Taxon
Known ClusterBlast
Sub ClusterBlast
MIBiG cluster comparison
Active Site Finder
ClusterBlast
Cluster Pfam analysis
RREFinder
Pfam-based GO term annotation
Cluster-border prediction based on transcription factor binding sites (CASSIS)
TIGRFam analysis
| additional options |
file
file
Binning
Marker Gene Sets
file
CheckM

Given one or multiple reference genome FASTA files, EDGE will turn on the analysis of the reads/contigs mapping to reference and JBrowse reference track generation. Given a reference genome genbank file, EDGE will also turn on variant analysis.

and/or

file Add
Read Aligner
Variant Call
Consensus Fasta
| additional options |

Consensus Generation Options

Disable BAQ
Remove PCR Duplicates
Homopolymer Filter
StrandBias Filter
Identify Unmapped Reads
Identify Unmapped Contigs

EDGE will try to classify reads and contigs that are unmapped to references by mapping them to NCBI RefSeq database.

Extract Mapped Reads
Extract Unmapped Reads
Ploidy

  1. Read-based Taxonomy Classification

    2. EDGE will use all reads by default. You can change the behavior to use reads that are unmapped to the reference if Reference-based Analysis is on.

    Always Use All Reads
    Classification Tools
    | additional options |
    Add
  2. Contig-based Taxonomy Classification
    3. Contigs Classification

EDGE supports 5 pre-computed databases for SNP phylogeny analysis and two tree builders. FastTree is faster and RAxML is slower but more accurate.

Tree Build Method

or

Select/Add Genomes or SRA Reads: The same species or at least within the same genus are recommended.

file Add
Bootstrap

  1. Read-based Gene Family Analysis

    2. EDGE will use ShortBRED to search the reads for Antibiotic Resistance genes from ARDB and Resfams and for Virulence genes from VFDB.

    Reads Gene Family Analysis
  2. Contig-based (CDS) Gene Family Analysis

    3. EDGE will use ShortBRED to search the CDSs on the contigs for Virulence genes from VFDB.

    EDGE will use RGI (Resistance Gene Identifier) to search the CDSs on the contigs for Antibiotic Resistance genes from CARD.

    CDS Gene Family Analysis
| additional options |

a. Primer Validation
b. Primer Design
Run Primer Validation

Given a primer file, EDGE will run validation of the primer pair to the reference and/or assembled contigs, as available.

file
Maximum Mismatch
Run Primer Design

EDGE will design primers based on the assembled contigs.

Parameters

  1. Barcode Options
    2. file
  2. Reads Quality Control and Feature Table Construction
    3. Quality Offset
    Quality Control Method
  3. Sampling
    4. Auto-Adjust Sampling Depth

Parameters

Platform
Mode
| additional options |

The following parameters will affect how the Quality Calcuation derived. The four weight parameters should sum up to 1. Mouse over the label to see the notes.

Parameters

  1. Required arguments
    2. Kingdom
    file
    file
    file
    file
  2. Optional arguments
    3. Strandedness
    file

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Max file size is 1gb. Allowed File types are fastq, fasta, genbank, gff, hmm, xlsx and text (txt,bed,config,ini) and can be in gzip format. Files will be kept for 7 days.

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