UFCG Pipeline - Manual

Current version: v1.0.5

Quick start

Conda

conda install -y -c bioconda ufcg
ufcg download -t minimum
ufcg -h

Docker

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

Manual installation

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

Requirements (manual installation)

Before installation, please make sure that the required programs are properly installed. Links for the installation of the requirements are listed in the download page.

• Java Runtime Environment with a version higher than 8
• Maven with a version higher than 3.9.4
• AUGUSTUS and MMSeqs2 are required for running profile module.

   Requirements - profile

  To run profile module, following binaries should run properly on your system: augustus fastBlockSearch mmseqs

  
  

  You can either record the path of these binaries on $PATH, or provide them as arguments of ufcg program.

  Got it
• MAFFT and IQ-TREE are required for running tree module.

   Requirements - tree

  To run tree module, following binaries should run properly on your system: mafft iqtree

  
  

  You should record the path of these binaries on a simple text file named tree.cfg such as:

  mafft=/path/to/mafft
  iqtree=/path/to/iqtree

  You can also use raxml or fasttree as a tree-builder; but you should specify the paths of these programs as well if you want to use them.

  Got it

Contents

Config files

• seq/ contains reference protein/nucleotide sequences of pre-defined genetic markers.
• model/ contains hidden Markov models, defined by protein sequences in seq/.
  • Detailed information of the genes are provided here.
• ppx.cfg is a config file used in gene prediction stage, utilized with AUGUSTUS.
• tree.cfg is a config file for tree module, containing path information of dependant binaires.

Samples

• Sample input and output files are prepared in sample/ directory. Visit tutorial page to learn how to use them.
• meta_*.tsv is a sample of TSV formatted metadata, which can be provided to the pipeline for annotating genomes.
  
  • More information about metadata is written in the Input files - Metadata section below.

Pipeline

• ufcg or ufcg.jar is an executable of the pipeline.

Input files

Genome assembly  

UFCG profile extracts the core gene profile from a FASTA formatted genome assembly.
A single assembly or a directory containing multiple assemblies are accepted as an input.

Metadata

You can provide a metadata for your input genome assemblies by converting them in a proper format. UFCG pipeline recieves seven entries that represents the taxonomic label of the genome.

bakers_yeast.fasta

Saccharomyces_cerevisiae_S288C

GCA_000146405.2

Saccharomyces cerevisiae

sacCer3

S288C

To provide the metadata to the pipeline, you should create a TSV (tab-separated values) formatted file including the data and specify it as an argument. TSV file must include the header line indicating entries, and respectively ordered metadata of the genomes one per line.

There are sample metadata TSV files prepared for your guidance. Visit tutorial page to find out how to use them.

• sample/meta_full.tsv contains fully constructed metadata of genomes in sample/seq/ directory.
• sample/meta_simple.tsv contains minumum data of the genomes.

Running profile module

Interactive mode

Run following command on your terminal to run UFCG pipeline interactively. Interactive mode will guide you through the options that pipeline requires, and automatically create the command to run the pipeline.

$ ufcg profile -u

Single line command

$ ufcg profile -i <PATH> -o <PATH> [options]

Results

The pipeline will extract the core gene profiles of given genome assemblies and store them as .ucg files.

• Note the path to the output directory, or copy its contents into the other directory, to use it as an input of tree module.

Running time

With 32 CPU threads, profile module requires about 55 seconds to extract the UFCG marker genes from a fungal whole genome assembly.

Running tree module

Align genes and infer tree

Run following command on your terminal to align the genes and infer phylogenetic tree with UFCG pipeline.

$ ufcg tree -i <DIR> -l <LIST> [options]

Results

tree module will produce following result files. You may further analyze the trees with various phylogenetic tools that can handle Newick files. (MEGA, ETE, ape, etc.)

concatenated.nwk

concatenated_gsi_[N].nwk

tree/[GENE].nwk

aligned_concatenated.fasta

align/aligned_[GENE].fasta

[run_id].log

[run_id].trm

Running time

With 32 CPU threads, tree module requires about 413 seconds to produce the trees from 30 UFCG profiles.

Replace labels of tree

Run following command to replace the name of leaves with a different format.

$ ufcg prune -i <TRM> -g <STR> -l <LIST>

Examples

To replace the UFCG tree by using taxon names and strain names as leaves from the run myRun, execute:

$ ufcg prune -i myRun.trm -g UFCG -l taxon,strain

To replace the RPB2 gene tree by using accessions and taxonomic relationships as leaves from the run Lorem_ipsum, execute:

$ ufcg prune -i Lorem_ipsum.trm -g RPB2 -l acc,taxonomy

Troubleshooting

Q. UFCG emits error "AUGUSTUS_CONFIG_PATH undefined or improperly defined". How can I solve it?

You have to define a local variable $AUGUSTUS_CONFIG_PATH to run AUGUSTUS properly. Run following code to define the variable.

$ export AUGUSTUS_CONFIG_PATH=/path/to/augustus/config/

If you are using bash, run this to semi-permanently add the variable on your system.

$ echo "export AUGUSTUS_CONFIG_PATH=/path/to/augustus/config/" >> ~/.bash_profile

$ source ~/.bash_profile

About us

UFCG pipeline was developed by Daniel Dongwook Kim.
UFCG project is under instruction of professor Martin Steinegger and Jon Jongsik Chun

© All rights reserved to Steinegger Lab, Seoul National University.