The Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite was developed with characterizing all domains of microorganisms as the primary objective (not post hoc adjustments) including prokaryotic, eukaryotic, and viral organisms. VEBA is an end-to-end metagenomics and bioprospecting software suite that can directly recover and analyze eukaryotic and viral genomes in addition to prokaryotic genomes with native support for candidate phyla radiation (CPR). VEBA implements a novel iterative binning procedure and an optional hybrid sample-specific/multi-sample framework that recovers more genomes than non-iterative methods. To optimize the microeukaryotic gene calling and taxonomic classifications, VEBA includes a consensus microeukaryotic database containing protists and fungi compiled from several existing databases. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and proteins to be directly compared across non-overlapping biological samples. VEBA also automates biosynthetic gene cluster identification and novelty scores for bioprospecting.
VEBA's mission is to make robust (meta-)genomics/transcriptomics analysis effortless. The philosophy of VEBA is that workflows should be modular, generalizable, and easy-to-use with minimal intermediate steps. The approach implemented in VEBA is to (try and) think 2 steps ahead of what you may need to do and automate the task for you.
In addition to the above, please cite the software dependencies described under the Dependency Citation Table.
The objective of VEBA is to provide high-quality metagenomics and metatranscriptomics workflows to the community. Understanding the user-base's needs will help me develop VEBA so it can make your research life easier.
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Current Stable Version: v2.2.0
Current Database Version: VDB_v7
If you are updating to v2.2.0 you will need to modify your existing database.
Please see FAQs for more details.
Installation and Database Configuration Guide for software installation and database configuration.
Usage and Resource Requirements Guide for parameters and module descriptions
Walkthrough Guides for tutorials and workflows on how to use VEBA
Visual Guides for video walkthroughs on how to use VEBA
Quick Guides for interpreting module outputs.
Test Data for testing installation/methods.
Usage Example:
e.g., Running preprocess
module.
1) Syntax compatible with Conda:
source activate VEBA
veba --module preprocess --params "{PARAMS}"
2) Syntax compatible with Conda and Docker/Singularity containers:
source activate VEBA-preprocess_env
preprocess.py "{PARAMS}"
Check out the VEBA Change Log for details between each update and insight into what is being implemented in the upcoming version.
VEBA's is built on the GenoPype archituecture which creates a reproducible and easy-to-navigate directory structure. GenoPype's philosophy is to use the same names for all files but to have sample names as subdirectories. This makes it easier to glob files for grepping, concatenating, etc. NextFlow support is in the works...
If perusing the Frequently Asked Questions doesn't address your question, feel free to submit a [Question
]