UPDATE: This tool now lives on GitHub
A friend in the lab needed to visualise coverage of metagenomic reads on a small genome and dnaplotter was not quite up to the task. It’s annoyed me for a while that there are at least two papers reporting fragment recruitment visualisation tools, but neither have actually published their code. Tsk tsk. So I knocked together a script which takes a reference genome and a BLAST output file (in -m 8 tabular format), and plots the read depth across the reference genome. You can also supply a simple comma-separated ”features file” and a “features” track will be added so you can see where key genes lie in relation to coverage.
Example output - click to magnify
The script supports smoothing of coverage by binning into windows of customisable size. For now it will only produce a linear plot but I’m working on circular. Requires R but no non-standard packages. Note that the script will plot every single hit in your BLAST table, so filter it to your specifications first. Get the code here:
https://github.com/wilkox/blast-tools
As always, feedback is very very welcome.
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[...] plot_coverage.pl now does plots of average percent identity of reads recruited to a genome. Get it while it’s hot. Don’t forget to email me or comment with your feedback. [...]
[...] perl script for plotting BLAST-based fragment recruitment against a reference sequence has been updated. You can now overlay up to five different queries on [...]