ginpipepy - Package for temporal binning of dated sequences in BAM format and fast population size estimate computation
This Python package is used by GInPipe [1] - Genome-based Incidence Estimation Pipeline. Functions implmented in ginpipepy are used to split aligned sequences in BAM format into chronologically sorted bins of predefined size and temporal length, and to calculate an estimate of population size. The package also includes a module for Variant Calling File reading that contains sites that have to be masked.
[1]
Smith, M. R. and Trofimova, M., et al. (2021). Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. medRxiv, https://github.com/KleistLab/GInPipe
ginpipepy - Package for temporal binning of dated sequences in BAM format and fast population size estimate computation
This Python package is used by GInPipe [1] - Genome-based Incidence Estimation Pipeline. Functions implmented in ginpipepy are used to split aligned sequences in BAM format into chronologically sorted bins of predefined size and temporal length, and to calculate an estimate of population size. The package also includes a module for Variant Calling File reading that contains sites that have to be masked.
Dependencies
ginpipepy uses the following packages:
Installation
ginpipepy can be installed using pip:
Reference
[1] Smith, M. R. and Trofimova, M., et al. (2021). Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. medRxiv, https://github.com/KleistLab/GInPipe