Repository for analysis of Syma torotoro and Syma megarhyncha genotype and phenotype data. A digital notebook recording commands for processing and analyzing data is found in pipeline.md.
(in scripts/ subdirectory)
assembly.R: Pipeline for assembling sequencing reads against Halcyon senegalensis draft genome.
genotype_analysis.R: Analysis of genotypic data and demographic inference output.
morphology_analysis.R: Analysis of morphological data.
msa.py: Commands to assembly and align mtDNA genomes.
oneliners.sh: Various bash oneliners.
plotting.R: Make figures for manuscript.
syma_*.py: Python scripts to generate joint site frequency spectra and fit demographic models in moments
unified_genotyper_all.sh: Command to run UnifiedGenotyper on all samples.
vocalization_analysis.R: Analysis of bioacoustic data.
(in data/ subdirectory)
Syma_*: Shape files for plotting range maps.
coverage.txt: Per-sample coverage.
meg_sizes.csv: Population size estimates for S. megarhyncha inferred from moments.
migration_rate.csv: Inferred rates of gene flow from moments.
morphology.csv: Morphological data from specimens.
params.csv: Bioacoustic parameter data.
percent_mapped.txt: Read mapping results.
syma_ND2.tree: ND2 tree.
syma_nd2_final.xml: BEAST .xml input file.
syma_spp_calls.csv: Processed bioacoustic data.
syma_spp_master.csv: Specimen, labwork data.
syma_spp_morphology.csv: Morphology data before processing.
syma_spp_morphology_log.csv: Log-transformed morphology data.
syma_spp_pcs.csv: PCA results.
syma_spp_pcs_old.csv: PCA results without modern samples.
syma_spp_pcs_wgs.csv: PCA results without hyRAD data.
tor_sizes.csv: Population size estimates for S. torotoro inferred from moments.