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assessPool example data
Freel
Zenodo (CERN European Organization for Nuclear Research)28 Aug 2024Open access
assessPool example data
Freel · Zenodo (CERN European Organization for Nuclear Research) · 2024
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Abstract
Example input VCF for assessPool. This VCF file was generated from pooled ezRAD samples of Montipora capitata collected at 10 different islands (one island per pool) in the Hawaiian Archipelago. Each pool consists of 24-57 indivudual samples, pooled equimolarly. Raw MiSeq reads were first trimmed using Trim Galore!, a de novo aseembled reference geneome (example_reference.txt) was assembled using SPAdes, and trimmed reads were mapped to this reference with bwa-mem. Varriant calling was performed using FreeBayes to generate the input VCF for assessPool. Additionally included is `example_fixed_samples.txt` used for an optional renaming step for each pool names in the VCF.