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Sequin Submission to Genbank Tutorial

5 minute read

Published:

Introduction

As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).

How-to: Simple ‘change over time’ maps in R

4 minute read

Published:

In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.

How-to: cancel a MrBayes run early

2 minute read

Published:

During my M.Sc. thesis I started to use the Bayesian phylogenetic MrBayes on clusters that do not make it feasible to keep open a terminal window. This meant I had to use ‘batch mode’, meaning I could only follow the status of the MrBayes run through the log files.

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teaching

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.

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.

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.