abelardoacm/ssDNA_viral_pangenomics

ssDNA viral pangenomics

in brief...

Viruses are a polyphyletic group. Due to the lack of common evolutionary markers among all viruses, artificial classifications not supported by evolutionary trees, have arisen. Furthermore, viral lineages present a large number of horizontal transport events with their hosts, thus carrying multiple genes of cellular origin defying classical evolutionary schemes.

The origin, or multiple origins of viruses is an inconclusive research topic that requires shifts in the classic paradigms and recent evolutive analysis tools.

This repository shows the workflow used to study the origin of single-stranded DNA viruses from an integrative perspective that makes use of pangenomics for the detection of relevant clusters for the group origins, alignment free methods for whole-genome comparisons, and phylogenetic inference methods compatible with network evolutionary schemes, allowing the incorporation of cellular protein sequences to perform remote homologues searches.

Cloning this repo

ssDNA_viral_pangenomics is a repository that depends on other github repositories. To avoid not allowed re-distribution of used files from those repositories, we included a .gitmodules file. Because of that, you should clone this repo as follows.

git clone https://github.com/abelardoacm/ssDNA_viral_pangenomics.git
cd ssDNA_viral_pangenomics/
git submodule init
git submodule update
cd bin/FSWM/
make
#To get mashv2.2 release if using Linux64
cd .. | mkdir mash
cd mash
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar
tar -xvf mash-Linux64-v2.2.tar

Dependencies

These are ssDNA_viral_pangenomics external dependencies, links to their installing instructions, commands for installation, and used versions:

Software name (version used)	Terminal	Installation *debian based dist.
EMBOSS (6.5.7)	bash	sudo apt-get install emboss
Biopython (1.78)	bash	sudo apt-get install python3-biopython
Numpy (1.19.4)	bash	sudo apt-get install python3-numpy
MATLAB (R2020b) + bioinformatics toolbox	bash	online installation via installation script
NbClust (3.0)	R (4.0.3)	install.packages("NbClust")
factoextra (1.0.7)	R (4.0.3)	install.packages("factoextra")
tidyverse (1.3.0)	R (4.0.3)	install.packages("tidyverse")
Corbi (0.6-1)	R (4.0.3)	install.packages("Corbi")
xts (0.12.1)	R (4.0.3)	install.packages("xts")

Install R dependencies by running install.packages(c("NbClust", "factoextra", "tidyverse", "Corbi", "xts"))
Install bash dependencies with sudo apt-get install emboss python3-biopython python3-numpy -y

Repo tree

These are the key repository folders :

.
├── bin <-  Contains scripts and dependencies
│
├── data
│   ├── AF_methods_input <- Aligment free methods input
│   ├── Genomic_fasta_files <- Individual fasta nucleotides genomic files
│   ├── Individual_full_genbank_files <- Individual full genbank files
│   ├── Mash_input <- Subfolders inputs to mash
│   ├── Proteomic_fasta_files <- Individual fasta aminoacids proteomic files
│   └── Raw_database <- Direct NCBI downloads
│
└── results
    ├── Clustering_graphics <- PCA's of clustering schemes
    ├── CPFSCC_vectors <- Cumulative fourier spectra vectors by family
    ├── Distance_Matrices <- Symmetric paired distances
    ├── Lists_for_sample_reduction <- List of n most distant files to delete
    ├── Mash_distances <- Mash output
    ├── Mash_sketches <- Mash midfile
    ├── Master_reports <- Summary of master script runs
    ├── NbClust_membership_vectors <- Text files with individual file membership
    └── Pangenomic_input_clusters <- Finall folders ready to serve as GETHOMOLOGUES input

NOTE* for storage purposes only files corresponding to Geminiviridae family are available. Whole database output will be available before research results submission

Repo navigation guide

Getting started

After cloning the repo, everything you need to get started are concatenated full genbank files in the Raw_database folder.

This folder should contain direct downloads from NCBI refseq.

Viral sequences can be searched family by family as follows, with the general query:

Family [ORGANISM] AND srcdb_refseq[PROP] NOT wgs[prop] NOT cellular organisms[Organism] NOT AC_000001:AC_999999[pacc]

Repo usage example

Below is an example of using all currently implemented steps, in a single call to the master script for the sample input of Geminiviridae family. when running, at the top of the terminal it will show which script is being performed. The master script needs some parameters to procceed and it even prompts hints to take particular decisions.

The outcome is summarized in a master report for the family, that you can find in results/Master_reports. It will save the selected parameters to perform each individual step, as well as the ins and outs locations.

Individual steps and details

The usage example only shows what happens when you call 0.1_Master_Driver.sh from bin and type the option 0 to perform all steps. However each step can be performed individually independent of the master script. For that purpose we've created a bin README file, that you can check here.