Yue Shi, Cory M. Dick, Kirby Karpan, Diana Baetscher, Mark J. Henderson, Suresh A. Sethi, Megan V. McPhee, Wesley A. Larson. Towards absolute abundance for conservation applications: estimating the number of contributors via microhaplotype genotyping of mixed-DNA samples. Molecular Ecology Resources, 00, 1– 13. https://doi.org/10.1111/1755-0998.13816
./data/alignment/: alignment summary.
./data/sam/: list of sam files. See ./scripts/slurm/ for alignment pipeline.
./data/meta/: sample meta info.
./data/panel/: panel info.
./data/microhaplot_input/: input files to run MICROHAPLOT.
./data/haplotypes/: output files from MICROHAPLOT.
./data/NOC/: NOC estimates.
./data/mock_subsamping_output/: results of DNA mixture subsampling experiments.
Note:
Demultiplexed GT-seq data used in this study are archived in the NCBI Sequence Read Archive with a BioProject ID, PRJNA917209. Consensus sequences (.fasta) and SNP info (.vcf ) of the microhaplotype panel with 125 markers used in the study to run MICROHAPLOT are archived on DRYAD (TBD).
./scripts/slurm/: slurm files for alignment to generate the list of sam files in ./data/sam/.
./scripts/:
1_panel_optimization.r: Fig S1.2_alignment_summary.r: Fig 1 and Fig S3.3.*_*.r: Fig S2.- run MICROHAPLOT to extract haplotypes from SAM files;
- conduct haplotype filtering;
- calculate haplotype frequency;
- check cross-contamination.
4.*_chinook_mockmix*: Fig 2, Fig 4, and Fig S4.5.*_*.r: Fig 3, Fig 5, and Fig S5.SeithSA_DNAMixture.r: likelihood-based model to estimate NOC in DNA mixtures.chinook_mockmix_subsampling_core.r: DNA mixture subsampling experiments.