This directory contains the pipelines and associated scripts used in the manuscript Extreme Y chromosome polymorphism corresponds to five male reproductive morphs by: Benjamin A Sandkam, Pedro Almeida, Iulia Darolti, Benjamin Furman, Wouter van der Bijl, Jake Morris, Godfrey Bourne, Felix Breden, Judith E. Mank.
The overall pipeline follows the order indicated on the filename: 1_Read_prep_and_De_novo_assembly.md 2_RACA_female_assembly.md 3_RACA_coverage.md 4_Ymer_identification.md 5_Ymer_phylogeny.md 6_Ymer_validation.md 7a_Male_Scaffold_Identification.md 7b_Male_Scaffold_annotation.md 8_Male_Scaffold_coverage.md 9_Autosomal_Phylogenies.md 10_Interspersed_Repeats.md
Script and pipelines have been annotated throughout and filenames must be adjusted as indicated. See manuscript for full details.
Note: Many of the steps require heavy computational power. We ran most of these pipelines on a system with 48 cores, 1.5Tb RAM, and 50Tb storage. A few pipelines were run on a desktop with 36 cores, 128Gb RAM, and 4Tb storage.
For further questions contact: Ben Sandkam - sandkam@cornell.edu