December 2022
Population assignment of Black-footed Albatross using GTseq and rubias.
Primers were designed from lcWGS data and will be used for:
(1) self-assignment of known-colony samples, and
(2) assignment of bycatch to breeding colonies.
Data are generated on a MiSeq at the AFSC Genetics Program lab in Juneau, AK,
bioinformatic analyses are performed on the NMFS HPCC, Sedna, based in Seattle, WA,
and finally, analysis of microhaplotypes, genotype data, and locus-fidelity is performed on Diana's laptop.
gtseq_test1 - 353 loci in a single primer pool, each at 0.25uM
gtseq_test2 - 351 loci in two separate primer pools, each at 0.25uM
gtseq_test3 - 284 loci in a single primer pool, with variable concentrations based on read depth results from test2
For identifying which primer pairs to keep in the pool and which ones to remove, I am looking at two primary characteristics:
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On-target reads - this is obtained through the GTscore analysis of merged vs. unmerged reads (R1 vs. Flashed reads)
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Read-depth - overamplifying primer sets should be removed or the concentration reduced.