MapperParameterVisualizer

This app allows researchers to evaluate the effect of command line parameter changes on Bowtie 2 and BWA-MEM alignments. Executing rshinyApp.R begins the Mapper Parameter Visualizer app. This a general description of the pipeline used to generate data:

1. Create the alignments using the scripts in bowtie2 and bwamem directories
2. Execute scripts in analysis_scripts
3. Run rshinyApp.R to visualize data

Description of Scripts

ART_simulate_reads.sh

script run to simulate Illumina paired-end reads using ART

generate_figures.R

script to generate all figures within the paper

rshinyApp.R

code for RShiny application

bwamem/bwa_miseq_run.sh and bwamem/bwa_simulated_run.sh

scripts for generating the BWA-MEM alignments with all different parameters

bowtie2/bowtie2_miseq_run.sh and bowtie2/bowtie2_simulated_run.sh

scripts for generating the Bowtie 2 alignments with all different parameters

Analysis Directory

For all scripts in the analysis_scripts directory, a primary script written in R or python is included as well as a bash script which shows how to execute the primary script. They are correspondingly named.

checkAccuracy

script used to compare the simulated read alignments to the correct ART alignment (written in python)

downsample

script used to downsample the depth of the reads (written in R) average is taken across 10,000 base pair windows

viewMappingQuality

script used to isolate the mapping quality distributions of all reads (written in python, corresponds to mapq.sh)