User:Megen002: Difference between revisions
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'''Main current projects''' | '''Main current projects''' | ||
* Genome sequencing of pig and turkey | * Genome sequencing of pig and turkey. | ||
* Re-sequencing projects on various livestock species | * Re-sequencing projects on various livestock species | ||
* Functional aspects of genome variation | |||
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 21: | Line 22: | ||
* Main sequencing platform is Illumina (We started in 2008 on Solexa GA, to currently Illumina HiSeq). | * 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) | * Depending on research questions various short-read mapping programs are used (Mosaik, BWA, BWA/Stampy, MrsFAST) | ||
* Variant calling | * Variant calling (Samtools, GATK). | ||
* Functional analysis of variants (Annovar, customly scripted tools) | * 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) | * Various population- and phylogenomic approaches to tackle specific questions (RAxML, Beagle, coalhmm, etc., and customly scripted tools) | ||
'''Main programming languages:''' | '''Main programming languages:''' | ||
* shell scripting | * Linux shell scripting | ||
* Perl | * Perl | ||
* Python | * Python | ||
| Line 32: | Line 33: | ||
* SQL | * SQL | ||
Favorite distros: Fedora/CentOS | Favorite distros: Fedora/CentOS, Ubuntu | ||
Revision as of 12:36, 11 December 2013
Hendrik-Jan Megens
- Profile on LinkedIn
- Profile on Google Scholar
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.
- Re-sequencing projects on various livestock species
- Functional aspects of genome variation
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:
- Linux shell scripting
- Perl
- Python
- R
- SQL
Favorite distros: Fedora/CentOS, Ubuntu