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 annotationsws11blastn.sh = bash script (196 cores) for annotating nucleotide sequences by blastn wordsize 11.blastx.sh = bash script for annotating nucleotide sequences by DIAMOND blasttrinity.sh = bash script for assembling high quality NGS reads into contigs by the Trinity algorithmabundance_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 analysislengths.csv = summary table of reference lengths generated by the abundance analysispcr.csv = summary table of RT-PCR confirmation heatmap2.Rmd = R script used for processing and visualizing the results of the abundance analysis.