Pipeline for Inferring Plastid Sequencing Depth and Evenness

A bioinformatic pipeline for inferring sequencing depth and evenness on complete plastid genomes

Description of Pipeline

This pipeline illustrates the individual steps taken during the analysis of sequencing depth and evenness of a set of 194 genome records of complete plastid genomes. The pipeline comprises of four parts: (i) read mapping, (ii) metadata extraction, (iii) calculation of sequencing depth and evenness, and (iv) statistical analysis.

Part i: Read mapping

Input: samples_list.csv

Conducting read mapping on a series of plastid genome records

#!/bin/bash

INPUT=/PATH/TO/samples_list.csv
OLDIFS=$IFS
IFS=','
[ ! -f $INPUT ] && { echo "$INPUT file not found"; exit 99; }
while read -r SRA SAMPLE ACCESSION;
do
bash ./read_mapping.sh $SAMPLE $ACCESSION $SRA </dev/null
done < $INPUT
IFS=$OLDIFS

Part ii: Metadata extraction

Input: samples_list.csv

Extract metadata of a series of plastid genome records

#!/bin/bash

INPUT=/PATH/TO/samples_list.csv
OLDIFS=$IFS
IFS=','
[ ! -f $INPUT ] && { echo "$INPUT file not found"; exit 99; }
while read -r SRA SAMPLE ACCESSION;
do
bash ./metadata_extraction.sh $SAMPLE $ACCESSION $SRA </dev/null
done < $INPUT
IFS=$OLDIFS

Part iii: Sequencing depth and evenness

Input: Customize path to resources in code

Gather all information into a single csv file.

Rscript depth_and_evenness.R

Part iv: Statistical analysis

Input: stats_ready_metadata.csv

Conduct statistical analysis on a series of plastid genome records

Rscript plastid_analysis.R