urfu_bioinf_2020

Pipeline for building of phylogenetic trees

Description

Using this pipeline you can create amazing phylogenetic trees of cell's channel. It's quite simple, you just need to add NCBI's indexes of genes or articles in the format html. At the output of the pipeline you can receive pictures with your phylogenetic trees. Pipeline can be configured for any phylogenetic tree creation.

The pipeline structure is here:

Denpendences

Snakemake
Matplotlib
Biopython
ClustalW
R
ggtree

Installation

You may use Docker but if you don't want to do it, make sure that you use R which is 3.6 version or later. Clone this repository to your workflow

git clone git@github.com:KonstantinUshenin/urfu_bioinf_2020.git

In the directory of this repository execute command for install dependencies for Python

pip install requirements.txt

After that compile libraries for R:

make

Usage

Make dir in folder dataset with name of your channel
In channel's directory add file with name request.txt and folder with name article/. In file request.txt add NCBI's indexes of nucleotides and add to folder article/ articles you are interested in
That's all. You can run pipeline by execute command

snakemake --cores=1 --forceall

Project structure

There are various folders in the project's directory:

dataset - contains folders with Ca and Na channels, which you may use as an example, here you can add your own channels
notebook_template - contains .py and .ipynb files which are neccessary for aligning sequences, building trees and visualization progress
pkg-source-files - contains packages for proper working with R
utils - contains commands for installing R dependencies and other utilites
workflow - a folder, which contains a result of a pipeline's work In the root directory you may see Snakefile and Dockerfile which you need to run in order to see the results of a pipeline.