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