Teaching

Methods Bootcamp Workshop: Mapping

Published in Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2017

This workshop was a part of the MPI-SHH ‘Methods Bootcamp’ seminar series, given by James A. Fellows Yates and Ron Huebler. This session introduced the basic concepts behind alignment, mapping of next generation sequencing DNA data and common programs used. We also gave practical examples of how different data compression techniques worked in these concepts.

Introduction to SLURM Workshop

Published in Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2017

This mini-workshop was given in March 2017 as an practical introduction on how to use SLURM on the MPI-SHH DAG computing infrastructure.

EAGER-MALT Crash Course Workshop

Published in Max Planck Institute for the Science of Human History, Department of Archaeogenetics, 2016

The aim of this crash course was to get those new to the MPI-SHH up to speed with some of the core tools that we are using in the institute, particularly for those working on pathogens. The workshop began with showing where to find internal documentation about the computing infrastructure and also how to access said infrastructure. Then, three (and a half) different programs were introduced and short practical examples given. The three programs discussed was - EAGER: our specialized pipeline for ancient DNA sequencing data pre-processing to genome reconstruction; MALT: a super-fast HTS read aligner used here currently for bacterial DNA screening; and MEGAN: a visualisation and analysis program for MALT results.