I have recently analyzed my metagenomic data using the metagenome-atlas. I have a set of MAGs of varying completeness/contamination and from different lineages and am looking for a way to visualize the coverage.
I have previously used BRIG before but not for coverage mapping, but I am aware that it does have a coverage mapping module. However, I am confused as to what my reference data would be.
I have also had some R packages recommended to me by colleagues (ggbio, circlize) but have no experience using these.
Any suggestions on what to use? Unfortunately I only have the atlas outputs because I do not have access to a server which can operate metagenome-atlas anymore.
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ellenphante •
If you don't have coverage information, that can be obtained on a per-contig basis by mapping the sequencing reads onto your metagenomic assembly.
Assuming you have some kind of embedding information for your bins - say coordinates from t-SNE or UMAP embedding - it becomes simply a matter of creating a scatter plot and coloring each dot by coverage values.
Looks great - do you have any tool suggestions to do this? I currently don't have coverage stats.
There are many tools to calculate contig coverage. I will recommend calculate_read_coverage.py from Autometa.
Making a plot like I did above is fairly trivial once you have [X, Y, coverage] columns. It is a scatter plot of [X, Y] colored by coverage values, which can be done using many tools such as pandas.plot.
If you want to analyze the coverage of you MAG trought the metagenomes you should use Anvi´o :) .... and if you want to see very quickly you can use anvi snakemate pipeline for metagenome analysis
https://merenlab.org/2018/07/09/anvio-snakemake-workflows/#metagenomics-workflow
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