User:Herrer01
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Juan Manuel Herrero Medrano
Postdoctoral position at Wageningen University, Animal Breeding and Genomics Centre.
Scientific interests:
- Bioinformatics
- Next Generation Sequence data and High-density SNP arrays analysis
- Functional genomics
- Population genomics
Main current projects
- Storage, mapping variants calling analysis on re-sequence data on various livestock species
- Functional aspects of genome variation in Turkey
- De novo assembly and annotation of genomes
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, Variant Effect Predictor)
- Various population- and phylogenomic approaches
Main programming languages:
- Linux shell scripting
- Python
- R