Krona snippet
I couldn’t find any kind of conversion Kraken and Krona recently and so I wrote up a little pipeline. Full script is available at lskScripts: https://github...
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Edirect snippets
I have been really excited by the new-ish edirect utilities. I thought I’d put out my snippets and encourage anyone to show theirs too. I haven’t found a l...
The confusing vocabulary of public health and bioinformatics
In the very beginning of our Listeria project, we basically had an idea that we could use evolution to help in epidemiological investigations. The idea was ...
Blog posts
A few blog posts that I’ve really liked for my niche of public health and bioinformatics. I think one purpose of this blog can be to start gathering these p...
FASTQ must die! Long live SAM/BAM! (seconded!)
Here is a short rant but it becomes proactive. For those of you who don’t know me, I dislike having two fastq files per genome if they are paired end (PE). ...