Copyright Jackson M. Tsuji, Neufeld Research Group, 2020
This Github repository describes the steps/code used to perform bioinformatics analysis for the paper by Tsuji and colleagues, "Anoxygenic photosynthesis and iron–sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes" (2020; ISME J article available here or 2019 biorxiv pre-print, titled "Genomic potential for photoferrotrophy in a seasonally anoxic Boreal Shield lake", available here). Descriptor files in this repo are in the Markdown (.md) format and begin with README. Other files include scripts and raw data files.
Describes the protocol used to produce assembled contigs and genome bins from the raw metagenomic datasets used for this paper.
Includes (some highlights):
01_data_acquisition- contains instructions for how to download the online sequencing data associated with this paper, including raw read data and genome bins04_HMM_development/02_alignment- contains an alignment of primary sequences of the Chlorobia-associated cyc2 genes identified in this study, plus reference cyc2 sequences04_HMM_development/03_HMMs- contains the custom HMMs developed in this study05_bin_analysis/03_metannotate/genome_bins- contains primary sequences of non-Chlorobia cyc2 genes detected in the lake metagenomes
A unique folder exists for most main or supplementary tables/figures in the publication, e.g., Figure_01_cyc2_genes. These describe the steps required to analyze the data for the figure and to generate a raw version of the figure for downstream editing.
Some supplementary material did not warrant having its own folder, so it is grouped in the Other folder in the same way that it would appear in the Supplementary Information on the journal website.
Note that this repo has a corresponding data repository in Zenodo for hosting larger files (e.g., non-curated genome bins). Check out the Zenodo version (v1.0.1) corresponding to the current Gitub repo code below:
Code in this repo shows how to use the files in the Zenodo repo for analysis.
It's likely that there are some typo's in the code. I did not perform all of these analyses at once, but I have tried in making this repo to organize them into one smooth, continuous workflow. This involved renaming some variables and such. Not all of the code has been tested in its current state.
If you want to try to use something here and are having problems (or have other questions/concerns about the analysis), feel free to post a Github issue.
If you'd like to cite this repo, then please cite the ISME J article:
Tsuji JM, Tran N, Schiff SL, Venkiteswaran JJ, Molot LA, Tank M, Hanada S, Neufeld JD. Anoxygenic photosynthesis and iron–sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. ISME J 2020:1-16.
I hope this is a helpful resource for the scientific community, both in the critique of my work and in further development of bioinformatics. Feel free to post an issue if you have any questions or concerns. Enjoy!
Jackson M. Tsuji
PhD Candidate
Neufeld Research Group
University of Waterloo
Waterloo, Ontario, CANADA