title: Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies.
abstract: BACKGROUND
  Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases. Despite the advent of next-generation sequencing technologies, Sanger sequencing is still the most popular approach in population genetics studies because of the widespread availability of automatic sequencers based on capillary electrophoresis and because it is still less prone to sequencing errors, which is critical in population genetics studies. Two popular software applications for re-sequencing studies are Phred-Phrap-Consed-Polyphred, which performs base calling, alignment, graphical edition and genotype calling and DNAsp, which performs a set of population genetics analyses. These independent tools are the start and end points of basic analyses. In between the use of these tools, there is a set of basic but error-prone tasks to be performed with re-sequencing data.
  
  
  RESULTS
  In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp.
  
  
  CONCLUSIONS
  We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses.
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Moara
authors.initials: M
authors.lastname: Machado
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Wagner Cs
authors.initials: WC
authors.lastname: Magalhães
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Allan
authors.initials: A
authors.lastname: Sene
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Bruno
authors.initials: B
authors.lastname: Araújo
authors.affiliation: Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Alessandra C
authors.initials: AC
authors.lastname: Faria-Campos
authors.affiliation: Laboratory of Translational Genomics of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, USA.|8717 Grovemont Circle Advanced Technology Center, Room 127, Gaithersburg, MD, 20877, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Chanock
authors.affiliation: Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil.
authors.forename: Leandro
authors.initials: L
authors.lastname: Scott
authors.affiliation: Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil.
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Tarazona-Santos
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil.
authors.forename: Maira R
authors.initials: MR
authors.lastname: Rodrigues