Beethoven

This repository contains a python package to recontruct queen genotypes from pool sequence data of honeybee hives. This implements the methods described in the paper:

From group to individual - Genotyping by pool sequencing eusocial colonies Sonia E Eynard, Alain Vignal, Benjamin Basso, Yves Le Conte, Axel Decourtye, Lucie Genestout, Emmanuelle Labarthe, Fanny Mondet, Kamila Tabet, Bertrand Servin bioRxiv 2021.11.08.467442; doi: https://doi.org/10.1101/2021.11.08.467442

Install the package

pip install .

should do it.

Run the scripts

Two scripts are provided. The first qg_pool allows to estimate the admixture proportions of the queen from the pool seq data

qg_pool -h

will give you the syntax to run the program.

The second genoqueen_hom is run like this:

genoqueen_hom dir_in depth.txt count_ref.txt n_col_snpid ncpu oprefix batch_len

• dir_in is the directory containing the input files
• depth.txt and count_ref.txt contain the depth and counts of the reference allele information for a set colonies. An example of 3 colonies with 1 SNP

$ cat depth.txt
rs12 1 290484 30 35 20
$ cat count_ref.txt
rs12 1 290484 15 5 18

• n_col_snpid is the number of columns to skip before reading counts/depth (3 in the example above)
• ncpu : number of CPUs to use
• oprefix : output prefix
• batch_len : size of batches that run in parallel (here 1000 SNPs).