We propose that the name for a group of MAGs (metagenome-assembled genomes) is a MAGstravaganza, like a gaggle of geese or a congress of owls. Using time-series metagenomes and time-series resolved MAGs from three different freshwater environments, we analyze predicted functions and how these function co-occur in genomes. This reveals how carbon and nutrient cycles are connected by microbes in freshwater.
The publication associated with this GitHub repo is: Linz AM, He S, Stevens SLR, Anantharaman K, Rohwer RR, Malmstrom RR, Bertilsson S, McMahon KD. 2018. Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 6:e6075 https://doi.org/10.7717/peerj.6075
Copyright (c) 2018, Katherine McMahon, Alex Linz, and friends
You're in the right place. Raw data is located in IMG (https://img.jgi.doe.gov/cgi-bin/mer/main.cgi) or on our lab fileshare.
- Use "IMG_Genome_ID" from the file "Publication/Supplemental_Data_S1.csv" to download the metagenomic time series.
- Use "IMG_Genome_ID" from the file "Publication/Supplemental_Data_S2.xlsx" to download MAGs.
- Use "IMG Genome ID" from the file "PublicationSupplemental_Table_S2.docx" to download pooled metagenome assemblies.
- If you're looking for intermediate files or code, check the list of files in this repo below.
Not seeing what you're looking for? Feel free to email us at amlinz@wisc.edu or trina.mcmahon@wisc.edu.
- README.md: This file
- Code/
- Tree_building/: Scripts to build a rough tree from MAGs. Full instructions available at https://github.com/McMahonLab/Scripts/tree/master/Phylogeny
- Functional_marker_genes/
- lefse_input.R: Code to take BLAST output table and format for input into LEfSe
- process_lefse_output.R: Code to turn LEfSe output into a dataframe suitable for R plotting
- Unused_analyses/
- chtc-kraken.sh: Code to run kraken on metagenomes in high throughput (not included in manuscript)
- kraken_report_processing.R: Code to take kraken output and make it into dataframes or plots
- thesis_pie_charts.R: Alternative view of MAG diversity made for A. Linz's thesis
- genome_size_figure.R: Initial testing of genome size vs. number of proposed substrates
- ANI_between_genomes.R: Make supplemental table of ANI from calculation output
- MAGstravaganza_manuscript_plots.R: Code to generate all plots in the manuscript
- amino_acid_bias.sh: Code to calculate amino acid bias from open reading frames
- process_tag_data.R: process .rData files that were output by TaxAss 16S classification
- time_series_mapping/
- Data files with metagenome information (ie dates, sizes, and library codes)
- Lake_results.txt files have the number of reads mapping to each MAG from each metagenome, and the size of the metagenome
- dbCAN2_results/
- Output of annotating CAZy enzymes in the MAGs, one file per MAG
- Mansucript_plots/
- Intermediate files of plots in the mansucript
- Pathway_analysis
- IMG_function_data.csv: annotations downloaded from IMG
- consolidated_pathway_data.csv/xls: aggregated pathway prediction data for input into Figure 3
- *.xls files with lake, phylum, and "pathways in the name are the pathway prediction files
- *.csv files with lake and phylum have pathway data aggregated by phylum
- split_by_lake_phylum.R: split the IMG_function_data by lake and phylum
- pathways_template.xls: Template for running pathway prediction. Paste IMG function data into the 1st worksheet to use.
- Supplemental/
- Assorted files used for supplemental tables, figures, and datasets. Mostly redundant with supplemental info accompanying the manuscript.
- Manuscript_drafts/
- MAGs_Manuscript_2018-06-28/
- The initial submission to PeerJ
- MAGs_Manuscript_revised_2018-10-22/
- The revised version re-submitted to PeerJ
- MAGs_Manuscript_revised_2018-11-01/
- The version accepted by PeerJ
- MAGs_Manuscript_2018-06-28/
- Publication
- Materials published by PeerJ