Copyright 2015-2017 -- Luca Freschi, Antony T. Vincent, Julie Jeukens, Jean-Guillaume Emond-Rheault, Irena Kukavica-Ibrulj, Marie-Josée Dupont, Steve J. Charette and Roger C. Levesque
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
SaturnV is a software that allows to compare two or more genomes in order to determine and study the core and accessory genes. The core genes are the set of genes that are present in all genomes of a given dataset. Unique genes (those present in one genome only) and flexible genes (those present in more than one genome) constitute the accessory genes.
SaturnV takes .fasta files as input (assembled genomes) and produces a matrix of presence/abscence for all the genes that constitute the pangenome of the species considered.
SaturnV is named after the [rocket][1] that brought humankind to the Moon in 1969. A bit like its space couterpart, SaturnV relies on several modules that have to function one after the other in order to achieve the objectives of the mission: determining, comparing and displaying core and accessory genes.
SaturnV was mainly written in Perl. Some parts are written in R and python.
Here is the complete list of dependencies that we are asking you to install in order to run the core module of SaturnV:
- perl + 3 perl libraries (Getopt::Long, Parallel::ForkManager, Graph)
- prokka (http://www.vicbioinformatics.com/software.prokka.shtml)
- usearch (http://www.drive5.com/usearch/ -- remember to download v8.x AND to rename the executable usearch8)
- GNU parallel (https://www.gnu.org/software/parallel/)
- seqtk (https://github.com/lh3/seqtk)
Other softwares you might want to install:
- last (http://last.cbrc.jp)
- blastp (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
If you have a Debian/Ubuntu installation (maning you have the command "apt-get" installed in your system), you can install most of the dependencies using this command:
sudo apt-get install libparallel-forkmanager-perl libgraph-perl libgetopt-simple-perl parallel seqtk
You just need to install prokka and usearch by yourself.
NOTE: SaturnV will use usearch as its default method to compare sequences. However, the same task can be performed by other softwares (i.e. blastp, last). SaturnV is ready to allow you to choose the software you are more confortable with. But you need to install these softwares too! :)
If you installed all the dependencies, you can proceed with the installation of SaturnV:
--step1: copy the saturnV repository to your computer. Open a terminal emulator, and type:
git clone https://github.com/ejfresch/saturnV.git
NOTE: you should have git installed! If it is not the case, please install it (hint for Debian/Ubuntu systems: sudo apt-get install git-core).
go into the directory saturnV with the command:
cd saturnV
--step 2: run the installer:
./install -d /home/lfreschi/sw/saturnv/ -m core
--step3: check that everything is OK. to check that everything went well, type satv_ and then hit the tab key twice. You should be able to see the whole list of SaturnV commands:
lfreschi@katak:~/tasks/pangenome/test_saturn/saturnv> satv_
satv_generate_list_genomes satv_search-pangenome-centroids satv_search-pangenome-lazy-best-hit
satv_launch satv_search-pangenome-laziest satv_search-pangenome-strictest
satv_prodigal-driver satv_search-pangenome-laziest-best-hit satv_trim-name-scaffolds
satv_prokka-driver satv_search-pangenome-lazy
[...the list continues if you installed two or more modules...]
If you are in trouble or you think you have followed all these steps but you just got some complicated error message, just write a message to l.freschi@gmail.com
SaturnV comes with a small dataset of Achromobacter genomes (n = 3). You can find them onto the directory examples/achromo/. We will use this dataset to go through the SaturnV commands and show you how you can use SaturnV to determine core and accessory genes.
--step1: create a working directory for the new analysis and create the subdirectory genomes/. Then copy the genomes you want to analyze into genomes/:
#I create the working directory
mkdir satv_test
#I move into it
cd satv_test
#I create the genomes/ directory
mkdir genomes
#I copy the genoms inside the genome directory
#NOTE: the files containing the genome assemblies MUST have the extension .fasta
#general synthax: cp <directory_where_you_installed_saturnV>/examples/achromo/* genomes/
#In my case:
cp ~/sw/saturnv/examples/achromo/* genomes/
--step2: launch the analysis
#general synthax: satv_launch -d <directory_genomes_to_analyze> -c <cpus_available_for_multithreading> -ann <annotation_software[prokka|prodigal]> -m <comparison_method[laziest|laziest-bh|lazy|lazy-bh|strictest|centroids]> -a <algorithm[usearch|blast|last]> -k <expression> -i <min_perc_identity_orthologs> -ip <min_perc_identity_paralogs>
#command to launch:
satv_launch -d genomes/ -c 2 -ann prodigal -m lazy -a usearch -i 50 -ip 100
--step3: look at the results
the main output is the table_linked5_<method>.tsv. When we launched saturnV, we specified to use the "lazy" method for the clustering step, so the file name will be table_linked5_lazy.tsv.
This file is a tab separated value (.tsv) file. In each row there is a gene and in each column there is its ortholog in another genome.
Another output is the annotation. By typing the command "ls" you will see that there are 3 folders, each one with the name of one of the genomes we analyzed. These folders contain the annotation (.gff file with the annotations, .faa with the proteins and so on).
If you use SaturnV to perform some data analysis for a scientific publication, please cite it using the URL of the project: https://github.com/ejfresch/saturnV.
NOTE: We are in the process of writing a paper to describe how SaturnV works and how it compares to other softwares that were written for the same purposes.