Rute da Fonseca
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When dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, a limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research in non-model organisms, they also demand unprecedented awareness from the researcher regarding the assumptions and limitations of each method.
In this review published in Marine Genomics we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analyses pipelines.
One of my main contributions to the bird phylogenomic effort was a tool to find problematic regions in the multiple sequence alignments, which was afterwards improved by Lisandra Zepeda and resulted in this companion paper.