User:Megen002: Difference between revisions
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[[File:HJM.jpg|right]] | [[File:HJM.jpg|right]] | ||
* Profile on [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=4846 We@WUR] | |||
* Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn] | * Profile on [http://www.linkedin.com/pub/hendrik-jan-megens/24/536/2b8 LinkedIn] | ||
* Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar] | * Profile on [http://scholar.google.nl/citations?user=kGUIXOYAAAAJ Google Scholar] | ||
Assistant Professor at Wageningen University, Animal Breeding and Genomics Centre. | |||
'''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) | ||
| Line 17: | Line 18: | ||
* 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. | ||
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'''Main programming languages:''' | '''Main programming languages:''' | ||
* Python | * Python | ||
* R | * R | ||
* Linux shell scripting | |||
* Perl (once upon a time....) | |||
* SQL | * SQL | ||
Favorite distros: Fedora | Favorite distros: Ubuntu, Debian, Fedora, CentOS, Raspbian | ||
== See also == | == See also == | ||
[[List_of_users | List of users of the HPC Agrogenomics]] | |||
Latest revision as of 13:42, 7 June 2017
Hendrik-Jan Megens
- Profile on We@WUR
- Profile on LinkedIn
- 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