bioedge update

[Lo, Chien-Chi]

Dear EDGE users,

We have updated the demonstration version of EDGE at https://bioedge.lanl.gov from the version 1.1 to development version. There are many features updates and bug fixes. The detailed change log can be found at https://raw.githubusercontent.com/LANL-Bioinformatics/EDGE/devel/ChangeLog.txt.  This webserver is for demonstration purposes and is restricted to use with either publicly available datasets via the SRA/ENA, or data available from the webserver. You can find the source code on the EDGE github development branch (https://github.com/LANL-Bioinformatics/EDGE/tree/devel). 

Thanks,

Chienchi

Highlight updates:

New modules:

1. Specialty Gene Profiling
2. Qiime pipeline for amplicon data analysis
3. Integration of metadata collection/storage
4. Comparison of multiple metagenomics samples’ taxonomy results

Updates:

1. R version 2.15.3 to 3.3.2,
2. KronaTools version 2.4 to 2.6,
3. Upgrade sratoolkit version from 2.4.4 to 2.8.1 which support proxy setup and https protocol
4. Update/Check metadata with SRA id and automatically retrieve metadata info from EBI ENA API
5. SPAdes from 3.5.0 to 3.9.1 (Add metaSPAdes, rnaSPAdes, plasmidSPAdes options for SPAades assembler)
6. Update project dir by using secure code instead of project id
7. Add email functions when job complete or shared to others
8. Separate [system] configruation from edge_config.tmpl into sys.properties.
9. MEGAHIT metagenome assembler.
10. Sample metadata Input
11. Many GUI features improvements: Add extract mapped reads fastq or mapped contig fasta function in the result table, Add Reconfig/rerun project action (beta), Sample Metadata actions: Add. Edit. Delete, Export as Excel, Add alt-click projectname to open in a new tab in project page and mouse over reminder, Add custom db input for reads taxonomy profiling 
12. Add MetaComp for multiple projects taxonomy result comparison as heatmap.(https://github.com/seninp-bioinfo/MetaComp.).

13. Clean intermediate files script for cron jobs set up.

    
    

Database update:

1. GOTTCHA db version v20150825
2. GOTTCHA2: euk-pathogen, euk-protozoa, euk-invertbrate
3. Host bwa index: pig, sheep, cow, monkey, hamster. and goat, rRNA, UniVec vectors, Plasmids