GUMPPGeneral Unified Microbiome Profiling Pipeline
• all involved programs are fully preconfigured
• preinstalled and preconfigured databases
• users can freely use their own databases
• customizable Mothur scripts for building biom and fasta files
• built-in repository of databases and scripts
• possibility to revert, complement or reverse-complement fasta file
• efficient utilization of computing resources
• suitable for autonomous and batch execution
• suitable for High-Performance Computing (HPC) facilities
• possibility of automatic crash recovery
• transparent handling of gzipped and unzipped reads
• automatic handling of intermediate files and their formats
• automatic handling of programs' command-line parameters
• experienced users can prescribe custom parameters
• efficient restarts with certain changes of workflow parameters
• complete screen and configuration dumping for easy documentation
• easy access to command lines, exit codes and messages of programs
• only meaningful output files are presented to a user
• ready-made inputs for Piphillin



Licensing:   Creative Commons Attribution CC BY licence
IMPORTANT. GUMPP is a workflow for a synergic execution of many externally developed pieces of software. These are disseminated as integrated parts of GUMPP to provide the level of end-user experience that the system aims to deliver. Nonetheless, every included piece of software remains owned and copyrighted by its respective developers.
Please see Credits in GUMPP Users' Manual for a list of included software.
IMPORTANT. GUMPP is developed and disseminated in a good faith and desire to work according to expectations, but authors DO NOT give any guarantees about its correctness. USE IT AT YOUR OWN RISK. Authors cannot be held legally or morally responsible for any consequences that may arise from using or misusing GUMPP.



Reference for citation
If you use GUMPP, please cite the following reference.
Murovec, B.; Deutsch, L.; Stres, B.

General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways.

Metabolites 2021, 11, 336.
Please also cite the included software that takes part in GUMPP's pipeline processing.
Please see Credits in GUMPP Users' Manual for a list of included software.



Download links
GUMPP workflow is available as a Singularity image, which may be run under Singularity version 3.x.
Please consult GUMPP Users' Manual for further instructions.
The most recent GUMPP version 1p was released on 5. 3. 2023 (summany of changes).
Download link for GUMPP 1P (5.4 GB).
Download link for GUMPP 1N (5.4 GB).
Please note. GUMPP image is fairly large because it contains all fully preconfigured programs and databases.
Optionally, advanced users may want to check integrity of downloaded GUMPP image by examining its SHA256 hash, which is calculated with the sha256sum utility.
To quickly start using GUMPP, please follow instruction in the Quick Start Guide.
To fully utilize GUMPP's capabilities, a more elaborate configuration file may be prepared according to the instructions in the GUMPP Users' Manual. A good starting point is the following configuration template file, which also includes a fair amount of comments and explanations.
Download link for GUMPP's configuration template file.
To make a test run of the GUMPP workflow, create a new directory within your home directory and download below demo configuration file into it. Then follow instructions within the file.
Download link for GUMPP's demo configuration file.



We look forward to receive your feedback regarding the use of GUMPP, potentially discovered bugs and issues, as well as comments and suggestions for further development of the system.
Blaž Stres   (metagenomic related topics)
University of Ljubljana, Biotechnical faculty, Slovenia
University of Ljubljana, Faculty of Medicine, Slovenia
UNI-LJ, Faculty of Civil and Geodetic Engineering, Slovenia

Institute of Microbiology, University of Innsbruck, Austria
Boštjan Murovec   (computing related topics)
University of Ljubljana, Faculty of electrical engineering, Slovenia
Leon Deutsch
University of Ljubljana, Biotechnical faculty, Slovenia