SCRIPTS

This repository contains the bash scripts and intermediate data files used during bioinformatics analysis.<br><br><b>merger.sh</b> = bash script for merging contigs from nucleotide and protein annotations<br><br><b>ws11blastn.sh</b> = bash script (196 cores) for annotating nucleotide sequences by blastn wordsize 11.<br><br><b>blastx.sh</b> = bash script for annotating nucleotide sequences by DIAMOND blast<br><br><b>trinity.sh</b> = bash script for assembling high quality NGS reads into contigs by the Trinity algorithm<br><br><b>abundance_analysis.tar </b>= 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.<br><br><b>counts.csv</b> = summary table of counts generated by the abundance analysis<br><br><b>lengths.csv</b> = summary table of reference lengths generated by the abundance analysis<br><br><b>pcr.csv</b> = summary table of RT-PCR confirmation <br><br><b>heatmap2.Rmd</b> = R script used for processing and visualizing the results of the abundance analysis.<br><br><br>