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Welcome to my GitHub page

I'm Jakob, a biologist-turned-programmer, happy in my role as a research software engineer.

I work as an assistant professor at CPR, Copenhagen University researching metagenomics with particular interest in virus- and plasmid metagenomics. Biologically, my interests are in phylogenetics, molecular evolution and sub-genomic replicons. On the computer science side, I'm a Julia, Rust and Python enthusiast, contributing to BioJulia and Julia. I particularly enjoy writing optimized and generic software packages for bioinformatics.

Highlighted work:

Blogposts

Selected repositories

Maintainer

Jakob Nybo Nissen's Projects

mgsop-binning icon mgsop-binning

Binning part of metagenomic standard operating procedure pipeline

micro icon micro

A modern and intuitive terminal-based text editor

minhash.jl icon minhash.jl

Fast and generic implementation of the minhash algorithm

ohmyrepl.jl icon ohmyrepl.jl

Syntax highlighting and other enhancements for the Julia REPL

phylo.jl icon phylo.jl

Simple phylogenetic trees in Julia to work with Diversity.jl - https://github.com/EcoJulia/Diversity.jl

pkg.jl icon pkg.jl

Pkg - Package manager for the Julia programming language

play icon play

Various scripts for fun and testing

plb2 icon plb2

A programming language benchmark

pycoverm icon pycoverm

Simple Python interface to CoverM's fast coverage estimation functions

question icon question

the question function, now in every language you could possibly want it in

revise.jl icon revise.jl

Automatically update function definitions in a running Julia session

sha.jl icon sha.jl

A performant, 100% native-julia SHA1, SHA2, and SHA3 implementation

smafa icon smafa

Biological sequence aligner for pre-aligned sequences

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