Population genomics

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In "Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods", du Plessis et al., 2023, 10.1093/molbev/msad207, the Cardfif team did population-genomics analyses on resequencing data of otter genomes (through ToL). The supplementary information contain a detailed listing (HTML) of the commands that were used to generate the analyses. Here is the PDF version: UK_bioinformatics_tobeshared.md.pdf.

There will be other population-genomics analyses in ToL and we should add the analyses that can be systematically run to the pipeline.

Task list

• Assess nf-core/sarek #79
• Assess Popgen48/scalepopgen #80
• Define test datasets for population genomics #81

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Consider these existing Snakemake workflows:

• https://github.com/jonahcullen/wags
• https://github.com/moiexpositoalonsolab/grenepipe
• https://github.com/harvardinformatics/snpArcher
• https://github.com/jkimlab/PAPipe