SARS-CoV-2-sequence-exploratory-analysis

This repository serves as a documentation on SARS-CoV-2 analysis trials. Different bioinformatic tools and experimental set up may be involved. This documentation will contribute to a transdisciplinary research project regarding SARS-CoV-2 evolution.

Environmnet set up

1. Download sequences from NCBI

ref sequence: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta

sample sequence: https://www.ncbi.nlm.nih.gov/nuccore/OP599898.1

2. Download MAFFT via conda

Assume that the conda environment is set up in the terminal, type the lines below to download the required tool, MAFFT.

conda install bioconda::mafft

mafft --help

The analysis can be done on local computer or on ssh server.

3. Biopython for sequence analysis (comparison)

available packages

from Bio import SeqIO from Bio.Seq import Seq from Bio.Data import CodonTable

import pandas as pd import numpy as np import matplotlib.pyplot as plt from sklearn import metrics import seaborn as sns import ete3