Workshop, 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.