User:Herrer01: Difference between revisions
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(Created page with "== Juan Manuel Herrero Medrano == Postdoctoral position at Wageningen University, Animal Breeding and Genomics Centre. '''Scientific interests:''' * Bioinformatics * Next...") |
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'''Main current projects''' | '''Main current projects''' | ||
* Storage, mapping variants calling analysis on re-sequence data on various livestock species | * Storage, mapping variants calling analysis on re-sequence data on various livestock species | ||
* Functional aspects of genome variation | * Functional aspects of turkey genome variation | ||
* De novo assembly and annotation of genomes | * De novo assembly and annotation of genomes | ||
'''Procedures''' | '''Procedures''' | ||
* 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). | ||
* | * Short-read mapping (Mosaik, BWA) | ||
* Variant calling (Samtools, GATK). | * Variant calling (Samtools, GATK, ANGSD). | ||
* Functional analysis of variants (Annovar, Variant Effect Predictor) | * Functional analysis of variants (Annovar, Variant Effect Predictor) | ||
* Various population- and phylogenomic approaches | * Various population- and phylogenomic approaches | ||
Latest revision as of 12:16, 19 February 2015
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 turkey genome variation
- De novo assembly and annotation of genomes
Procedures
- Main sequencing platform is Illumina (We started in 2008 on Solexa GA, to currently Illumina HiSeq).
- Short-read mapping (Mosaik, BWA)
- Variant calling (Samtools, GATK, ANGSD).
- Functional analysis of variants (Annovar, Variant Effect Predictor)
- Various population- and phylogenomic approaches
Main programming languages:
- Linux shell scripting
- Python
- R