fastAPD_workflow

Nucleotide diversity (average pairwise difference) workflow

This workflow makes use of the Bio::fastAPD Perl module for fast calculations of nucleotide diversity (average pairwise difference (APD)) from multiple sequence alignments. The workflow accompanies the following peer-reviewed journal article:

Julian TR, Baugher JD, Rippinger CM, Pinekenstein R, Kolawole AO, Mehoke TS, Wobus CE, Feldman AB, Pineda FJ, Schwab KJ. Murine norovirus (MNV-1) exposure in vitro to the the purine nucleoside analog Ribavirin increases quasispecies diversity. Virus research. 2016 Jan 4;211:165-173.

Requirements

This workflow has been tested on MACOSX and linux operating systems using recent versions of Perl, R, and X11.

Perl modules:

Bio::fastAPD v1.10.0 or higher

R libraries:

ggplot2

Data for Analysis

A subdirectory named data may be created in the fastAPD_workflow directory to house the data for analysis.

Usage

To run the analysis - From within a shell session, navigate to the fastAPD_workflow directory and type:

bash nucleotide_diversity.sh ./data

The analysis consists of four steps. The user will be notified when the script has finished. If no errors are reported, the analysis is complete.

Authors

Joseph D. Baugher, Ph.D. and Fernando J. Pineda, Ph.D.
Copyright (c) 2014,2015 Joseph D. Baugher, Ph.D.

Maintainer

Joseph D. Baugher, Ph.D., joebaugher(at)hotmail.com