User:Megen002

Hendrik-Jan Megens

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Senior Researcher and lecturer at Wageningen University, Animal Breeding and Genomics Centre.

Scientific interests:

Coming from a wet-lab background I discovered I had more talent for programming than for pipetting. I have moved into applied bioinformatics in the past 7 years, while retaining focus on my research interests:

• evolutionary genomics (generation and maintenance of, and selection on, structural and single nucleotide variation; speciation and outbreeding depression; inbreeding depression and heterosis)
• population genetics (genetic consequences of population management, domestication, selection)

Main current projects

• Genome sequencing of pig and turkey (genetic map construction, repetitive element evolution)
• Re-sequencing projects on various livestock species

We are currently sequencing >300 pigs, wild boar, and outgroup species. The project aims to elucidate major patterns in biogeography and domestication of the pig, resulting from selection and demography.

Procedures

• Main sequencing platform is Illumina (We started in 2008 on Solexa GA, to currently Illumina HiSeq).
• Depending on research questions various short-read mapping programs are used (Mosaik, BWA, BWA/Stampy, MrsFAST)
• Variant calling is done mostly by SamTools, but we are currently investigating other software (GATK).
• Functional analysis of variants (Annovar, customly scripted tools)
• Various population- and phylogenomic approaches to tackle specific questions (RAxML, Beagle, coalhmm, etc., and customly scripted tools)

Main programming languages:

• shell scripting
• Perl
• Python
• R
• SQL

Favorite distros: Fedora/CentOS