UFCG pipeline

UFCG pipeline provides methods for a genome-wide taxonomic profiling and annotation of your own biological sequences of Fungi.

• Homepage
• Publication

How to cite

Kim, D., Gilchrist, C.L.M., Chun, J. & Steinegger, M. (2023) UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research, 51(D1), D777-D784, doi:10.1093/nar/gkac894.

Installation

Quick start with conda

conda install -y ufcg # conda-libmamba-solver recommended
ufcg download -t minimum
ufcg -h

Quick start with docker

docker pull endix1029/ufcg:latest
docker run -it endix1029/ufcg:latest
ufcg -h

Build from source

Build requirements

• Java 8 or higher
• Maven 3.9.4 or higher

Build

git clone https://github.com/steineggerlab/ufcg.git
cd ufcg
mvn clean package appassembler:assemble
./target/bin/ufcg -h

Runtime requirements

• Java 8 or higher
• profile - AUGUSTUS v3.5.0 or higher
• profile - MMseqs2 v13 or higher
• tree - MAFFT v7.310 or higher
• tree - IQ-TREE v2.0.3 or higher

Modules

profile

UFCG profile extracts marker gene sequences from your own Fungal biological data, including genome sequences, transcriptome sequences, and proteome sequences.

• Interactive mode

ufcg profile -u

• I/O mode

ufcg profile -i <INPUT> -o <OUTPUT> [OPTIONS]

tree

UFCG tree reconstructs the phylogenetic relationship of the set of marker gene profiles.

ufcg tree -i <INPUT> -o <OUTPUT> [OPTIONS]

train

UFCG train generates sequence model of your own fungal marker gene, even from a small set of seed sequences.

ufcg train -i <INPUT> -g <REFERENCE> -o <OUTPUT> [OPTIONS]

align

UFCG align conducts multiple sequence alignment of the genes from the set of marker gene profiles.

ufcg align -i <INPUT> -o <OUTPUT> [OPTIONS]