Antti Karkman's Projects
An analysis and visualization platform for 'omics data
The anvi'o community web page
Demo binder repo
Rstudio binder for courses
Source code for the crAssphage project
Poster for EDAR7 conference
Instructions and examples for how to analyze epicPCR data
Exercise to practice collaborative forking workflow.
Git repo for the Fundamentals of Machine Learning Course
Parser to add external gene calls and functional annotation from Prokka to Anvi'o.
Data analysis for Global Sewage project
template for IODS course projects
Demo workflow for 16S rRNA data analysis
Course repository for the spring 2022 MBDP genomics course
Course repository for MBDP metagenomics course 2022
Course material for the metagenomics course
Metagenomics course
Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017
Whole genome analysis teaching for the course 'MMB-114 Exploratory microbial research - lab course' of the University of Helsinki.
Environmental microbiology course
Course repository for Environmental microbiology course (MMB-117) at the University of Helsinki.
MMB-901 metagenomics course repository
Repository for pangenomics teaching demonstration
A simple script to parse DIAMOND results in to a data frame
pb-metagenomics-tools
Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and John D. Coates. (2018) Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities.
Environmental metagenomics, Spring 2022, Physalia Courses
Environmental metagenomics, Spring 2023, Physalia Courses
Environmental metagenomics, Spring 2021, Physalia Courses