Michael Gerth
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Two new scripts for creating simple GC-coverage plots from SPAdes assemblies and analysing PhyloBayes trace files

18/12/2017

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Before writing about science again (new post is in the making), I have uploaded two scripts that I find useful for my work:
​

gc_cov.pl 

This script is basically a very simplified version of the blobplots function from the BlobTools package. It creates GC-coverage plots directly from SPAdes assembly files, without the need for mapping the reads back to the assembly. Since I use mainly SPAdes anyway, this has been quite handy. The script will also annotate the plot when a taxonomy file is provided, which can be generated, e.g., from blast outputs. Below is an example for the plots that can be generated with the script.
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    This is the website of Michael Gerth. I am a biologist with an interest in insects and the microbes within them. Click here to learn more.

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  • News & Blog
  • About
  • Research
    • Experimental evolution of Spiroplasma after host shifts
    • Wolbachia phylogenomics
    • Rickettsial symbionts in green lacewings
    • The role of Wolbachia in quill mites
    • Methods in molecular phylogenetics
  • Publications
  • Resources