npstat : An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data
Ramos Onsins, Sebastián Ernesto (Centre de Recerca en Agrigenòmica)
Guirao-Rico, Sara (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Hafez, Ahmed (Parque Tecnológico de Paterna. Biotechvana)
Ferretti, Luca (University of Oxford. Nuffield Department for Medicine)

Imprint:	New York : Humana, 2025
Abstract:	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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Language:	Anglès
Series:	Methods in Molecular Biology ; 2935
Document:	Capítol de llibre ; recerca ; Versió acceptada per publicar
Subject:	Polymorphism ; Divergence ; Population genomics ; Proportion of beneficial substitutions ; Sliding window analyses
Published in:	Insect Genomics. Methods and Protocols, 2025, p. 51-66, ISBN 978-1-0716-4583-3

DOI: 10.1007/978-1-0716-4583-3_3

Available from: 2026-08-31 Postprint 23 p, 932.4 KB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Books and collections > Book chapters