The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes - accompanying code and scripts.

Github repository accompanying the publication titled The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. These scripts were utilized in the analyses presented in the publication.

Preprint

The preprint is currently available at. https://www.biorxiv.org/content/10.1101/2023.11.30.569198v1

Links to tools from other repositories used within the paper.

https://github.com/abcsFrederick/non-B_gfa \ https://github.com/agshumate/Liftoff \ https://github.com/arangrhie/T2T-Polish/tree/master/marker_assisted \ https://github.com/asl/BandageNG \ https://github.com/ComparativeGenomicsToolkit/cactus/releases/tag/v2.6.0 \ https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit \ https://github.com/Dfam-consortium/RepeatModeler \ https://github.com/epi2me-labs/modbam2bed \ https://github.com/fedorrik/apeXY_hmm \ https://github.com/fedorrik/stv \ https://lastz.github.io/lastz/#fmt_rdotplot \ https://github.com/kxk302/Non_B_DNA_vs_novel_bar_plot/tree/XY_Paper \ https://github.com/maickrau/ribotin \ https://github.com/mrvollger/rustybam \ https://github.com/rmhubley/RepeatMasker/tree/master/util \ https://github.com/santiagosnchez/vcf2fasta \ https://github.com/thackl/minidot \ https://github.com/wharvey31/saffire_sv