Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies

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.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.Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows screening of variation in a way that is unbiased in respect to the allele frequency spectrum and because it is suitable for a wide variety of living organisms. Although there is a plethora of new opportunities from next-generation sequencing (NGS) technologies [1], re-sequencing studies are traditionally performed using Sanger DNA sequencing. This is due, in part, to the widespread availability of automatic sequencers based on capillary electrophoresis and also to the fact that Sanger sequencing is still less prone to base-calling errors [2], which is critical in population genetics studies for which the accurate identification of substitution