Two new scripts for creating simple GC-coverage plots from SPAdes assemblies and analysing PhyloBayes trace files
Before writing about science again (new post is in the making), I have uploaded two scripts that I find useful for my work:
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.
I have written a small script that automates the download of fastq files from the European Nucleotide Archive (ENA). This was created because I was annoyed with the speed NCBI's sra-tools. It takes NCBI SRA accession numbers as input and downloads the fastq files directly from the ENA using wget. The download speed is thus basically only limited by your bandwidth. Any feedback is very welcome!
Find it on the resources page or on github.
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.