Category Archives: software

A short list of tools for shotgun metagenomics

We are currently finalizing our work on the analysis of metagenomes for soils taken from the Etosha National Park, Namibia. These soils were interesting since Zebra blood containing the nasty bug Bacillus anthracis had poured into it. Our aim was … Continue reading

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Gzip vs Bzip2. Some notes when moving files from Windows 7 to Mac OSX

For a metagenomic bioinformatics course I needed to created a Virtual machine (VM) with all software that will be used during the course. For this I started with the QIIME Virtual machine disk , since it has already a nice … Continue reading

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Removing small & low coverage contigs from a Spades assembly

At the moment I am processing quite a few bacterial genome assemblies that I created for various Thermotogae species. I am comparing assemblies created by CLC, Velvet and the latest SPAdes assembler with REAPR. Both CLC and Velvet were set … Continue reading

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Installing phiSpy on my macbook.

The reason for this post is that in my current project I need to identify prophages in Thermotogales genomes. Prophages are phages /virusses that are integrated into the genome of their host, in our case Bacteria. To check if our … Continue reading

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