This repo represents a collection of scripts for genome assembly, phylogenomics and genomic variation assessment in mustelids, accompanying the manuscript Derežanin et al. (2022) "Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae", and sequencing data available under the NCBI Project ID: PRJNA732552. Manuscript currently under revision (Molecular Ecology), preprint available at bioRxiv, DOI: doi.org/10.1101/2021.09.27.461651.
- 01_Genome_assembly - 10xGenomics linked-reads preparation, assembly runs, genome metrics (autohor: Lorena Derezanin)
- 02_Phylogenetics - parsing nucleotide sequence alignments and estimating species divergence time (author: David A. Duchene Garzon)
- 03_Gene_family_evolution - inferring gene gains/losses from BUSCO output (authors: Lorena Derezanin and Dorina Meneghini)
- 04_Structural_variation - snakefiles with ordered steps for sequence preparation, structural variant calling, and functional annotation (author: Lorena Derezanin)
Additional scripts can be found at https://github.com/mahajrod/MACE