UFCG pipeline provides methods for a genome-wide taxonomic profiling and annotation of your own biological sequences of Fungi.
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.
conda install -y ufcg # conda-libmamba-solver recommended
ufcg download -t minimum
ufcg -h
docker pull endix1029/ufcg:latest
docker run -it endix1029/ufcg:latest
ufcg -h
- Java 8 or higher
- Maven 3.9.4 or higher
git clone https://github.com/steineggerlab/ufcg.git
cd ufcg
mvn clean package appassembler:assemble
./target/bin/ufcg -h
- Java 8 or higher
profile
- AUGUSTUS v3.5.0 or higherprofile
- MMseqs2 v13 or highertree
- MAFFT v7.310 or highertree
- IQ-TREE v2.0.3 or higher
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]
UFCG tree
reconstructs the phylogenetic relationship of the set of marker gene profiles.
ufcg tree -i <INPUT> -o <OUTPUT> [OPTIONS]
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]
UFCG align
conducts multiple sequence alignment of the genes from the set of marker gene profiles.
ufcg align -i <INPUT> -o <OUTPUT> [OPTIONS]