poolStat

poolStat is a tool to work with pooled sequencing data. It differs from the commonly used tool popoolation in that it allows to build pipelines that account for sequencing errors.

Installation and basic usage

Please follow the detailed instructions given here: Installing and Running poolStat

##Known Sample Sizes (classic poolSeq)

If you conducted a classic poolSeq run in which a known number of diploid individuals where pooled onto a single sequencing lane, we recommend analyzing this data by using Allele Frequency Likelihoods (AFL) as detailed here: Allele Frequency Likelihoods (AFL)

##Unknown Sample Sizes

poolStat also implements some routines to work with pooled data in which an unknown number of individual where pooled (e.g. from a bacterial swap). These routines are outlined here: Stats from MLE frequencies