SCRIPTS

This repository contains the bash scripts and intermediate data files used during bioinformatics analysis. merger.sh = bash script for merging contigs from nucleotide and protein annotations ws11blastn.sh = bash script (196 cores) for annotating nucleotide sequences by blastn wordsize 11. blastx.sh = bash script for annotating nucleotide sequences by DIAMOND blast trinity.sh = bash script for assembling high quality NGS reads into contigs by the Trinity algorithm abundance_analysis.tar = archive of text files containing the commands used for abundance analysis. Briefly, taxon-binned contigs are collected and build into a reference for subsequent HISAT2 aligment of forward NGS reads. counts.csv = summary table of counts generated by the abundance analysis lengths.csv = summary table of reference lengths generated by the abundance analysis pcr.csv = summary table of RT-PCR confirmation heatmap2.Rmd = R script used for processing and visualizing the results of the abundance analysis.