User:Megen002: Difference between revisions
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'''Scientific interests:''' | '''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 | Coming from a wet-lab background I discovered I had more talent for programming than for pipetting. I have moved into applied bioinformatics since 2004, 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) | * 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) | * population genetics (genetic consequences of population management, domestication, selection) | ||
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* Re-sequencing projects on various livestock species | * Re-sequencing projects on various livestock species | ||
* Functional aspects of genome variation | * Functional aspects of genome variation | ||
* De novo assembly and annotation of genomes | |||
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. | 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. | ||
| Line 30: | Line 31: | ||
'''Main programming languages:''' | '''Main programming languages:''' | ||
* Python | * Python | ||
* R | |||
* Linux shell scripting | * Linux shell scripting | ||
* Perl | * Perl (once upon a time....) | ||
* SQL | * SQL | ||
Latest revision as of 13:42, 7 June 2017
Hendrik-Jan Megens
- Profile on We@WUR
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- Profile on Google Scholar
Assistant Professor 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 since 2004, 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.
- Re-sequencing projects on various livestock species
- Functional aspects of genome variation
- De novo assembly and annotation of genomes
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 (Samtools, 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:
- Python
- R
- Linux shell scripting
- Perl (once upon a time....)
- SQL
Favorite distros: Ubuntu, Debian, Fedora, CentOS, Raspbian