Rock_Creek_Shotgun_Metagenomic_Analysis

Metagenomic sequence assembly, binning, functional/taxonomic annotation, reads quantification, and data analysis

Notes:

This repository is associated with the preliminary analysis of the shotgun metagenomic sequencing data for a few selected samples. More samples are being sequenced and analyzed.

Contents

Directory bioinformatic_bash_files/ contains the bash files used to call MetaWRAP modules and other bioinformatics software to process the shotgun sequencing data. Directory data_analysis_files/ contains the Python and R codes for downstream data analysis and visualization.

Contents of bioinformatic_bash_files/ :

• annotate_bins_using_metawrap.sh : functional annotation of MAGs
• assembly_metawrap.sh : de novo assembly
• bin_refinement_using_metawrap.sh : consolidate of multiple binning predictions into a superior bin set
• binning.sh : initial bin extraction with MaxBin2, metaBAT2, and CONCOCT
• binning_to_end.sh : a shell wrapper to run binning, bin_refinement and reassembly sequentially
• classify_bins_using_GTDB-Tk.sh : taxonomic classification of bins with GTDB-Tk
• classify_bins_using_metawrap.sh taxonomic classification of bins with metawrap module
• concatenate_bins.sh : concatenate each bin.fa file into one all_bin.fa file
• prokka_on_all_scaffolds.csh : functional annotation of contigs using Prokka
• reassembly_using_metawrap.sh : reassemble bins to improve completion and N50, and reduce contamination
• rename_bin_to_fna.sh : changes the suffix of bins from .fa to .fna to fulfill GTDB-Tk input requirements
• salmon_on_bins.sh : estimate bin abundance across samples
• rename.sh : change sample name to meaningful names

Contents of data_analysis_files/ :

• match_contig_to_bin.py : produce a .txt file that links bin.faa file to the associated contig IDs
• salmon_combine_tpm_results.py : parse the salmon output and generate a .csv file showing the TPM of each locus in every sample
• morris_gene_selection.py : select locus associated with targeted KEGG numbers
• shorten_contig_names.py : shorten the contig names
• dir environmental_sample_analysis: R codes, inputs and visualization of the taxonomic/functional annotation of bins
• dir zymo_community_analysis : R codes, inputs and visualization of the comparison of the positive control sample (zymo community) between theoretical values and results