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