Kākāpō Genotyping-by-sequencing (GBS)

Foster et al. 2021. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō.

G3 Genes|Genomes|Genetics. https://doi.org/10.1093/g3journal/jkab307

Genotyping-by-sequencing (GBS) performed at AgResearch Invermay (New Zealand) for Strigops habroptilus, the kākāpō parrot.

Single-ended and double-digested with MspI and PstI.

Alignment with BWA, referenced-based SNP calling with Stacks, filtering with VCFtools, and population genomic analyses estimating inbreeding.

1- SNPcalling.md: demultiplexing, pre-processing (trimming & quality control), alignment, and referenced-based SNP calling

2- SNPfiltering.md: post SNP-calling filtering for depth and missing data

3- Inbreeding.md: multiple methods for estimating inbreeding metrics

Email for questions: y.al.foster@gmail.com OR yasmin.foster@postgrad.otago.ac.nz

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Female kākāpō, Lisa. A Stewart Island founder.

Photo: Jake Osborne. Kākāpō field ranger extraordinaire.

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