Pool sequencing has emerged as a valuable approach in ecological studies, particularly when dealing with very small organisms (with limited amount of DNA available), when distinguishing individual organisms is a challenge (e.g., in colonies, microbiome), when there is a trade-off between the sequencing cost and the number of individuals to sequence, when the main goal is to estimate nucleotide variability and variant frequency patterns at the population level (that is, when individual information is not required). Estimates of variability can be efficiently explored by analyzing sequences of pooled individuals sampled from the population. When using this approach, the number of pooled individuals and the mean read depth are key choices in the experimental design.The software npstat calculates different estimates of nucleotide variability and neutrality tests.It also calculates the number of synonymous and nonsynonymous variants and the proportion of beneficial substitutions (alpha) using the MKT approach when GTF annotation file and an outgroup is provided.
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Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones CientÃficas-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-University of Barcelona, Bellaterra, Spain. sebastian.ramos@cragenomica.es.
Sequence Analysis, DNA, Computational Biology, Genetics, Population, Software, Genetic Variation, High-Throughput Nucleotide Sequencing