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Data analysis by imputation of EXTREME-LOW coverage sequencing (EXL-WGS): markers detection and population genetics

Grant number: 18/07406-6
Support Opportunities:Scholarships in Brazil - Master
Effective date (Start): June 01, 2018
Effective date (End): April 30, 2020
Field of knowledge:Biological Sciences - Parasitology - Entomology and Malacology of Parasites and Vectors
Acordo de Cooperação: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal Investigator:Paulo Eduardo Martins Ribolla
Grantee:Marcus Vinicius Niz Alvarez
Host Institution: Instituto de Biotecnologia (IBTEC). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil


Projects demanding for large scale whole genome sequencing (WGS) are often impractical due to the cost of the technique when applied in large sample quantities. Therefore, studies are needed to find new viable and low-cost strategies that can be adopted to circumvent the situation. The objective of this project is to study different methods of obtaining genomic information from WGS of extreme low coverage (EXL-WGS) to study populations. Larvae and adults of Anopheles Darlingi in different environment conditions were captured in Mâncio Lima - AC. The Nextera XT (Illumina) protocol was performed with 1/5 of the volume suggested by the standard protocol and the DNA sequenced by the NextSeq500 (Illumina). Genotyping by sequencing and imputation of the markers will be performed for population study, correlating with different collection conditions, such as time and location of capture. (AU)

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Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
ALVAREZ, Marcus Vinicius Niz. Low coverage sequencing data analysis using imputation: Marker selection and population genetics.. 2020. Master's Dissertation - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.

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