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Snakemake k-mer

Description

Use of Snakemake workflow management system along with k-mer algorithm.

K-mers are subsequences of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides (i.e. A, T, G, and C), k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines.This project evaluate parameters of specific k and choose the best k for the DNA sequences.

Requirements

Before you continue, ensure you have make sure the following packages are installed in your local machine:

  • You have installed the python libraries:
    1. Natural Language Toolkit library.
    2. Scikit-learn library.
    3. Seaborn library.

Installation

To install Snakemake k-mer project:

  1. Click the Code Bar and download the zip file of the project.

Or

  1. You can clone the project in your local PC using git:
    git clone https://github.com/seramelp/Snakemake-k-mer.git

Geting started

The project consists of one main file:

  • Snakefile

and eight additional scripts, that contain the functions called by the main file:

  • k-mer.py
  • fit.py
  • best-fit.py
  • matrix.py
  • plot.py
  • count_kmers.py
  • godel_f.py
  • dataPreProcessing.py

In order to run the project follow the steps:

Step 1. Remove the default .fasta file from files directory and Copy yours .fasta file in files directory.
Step 2. Modify the variable k in Snakefile file with the choosen integer numbers for the analyses.
Step 3. Run the command line snakemake in a conda enviroment.
Step 4. Wait for the results.

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