This project realigns reads from publicly available genomes to the new Telomere-to-Telomere (T2T) CHM13-HG002 reference genome.. Open Genomes Telomere-to-Telomere (T2T) Reference Realignment Project

This project makes available alignments of publicly available read data from trom the Genome In a Bottle Project, the Human Pangenome project, the 1000 Genomes Project, and the HGDP, among others, to the new Telomere-to-Telomere (T2T) v.1.1 Reference combined with the new T2T Y chromosome reference CP086569.1, which creates for the first time a complete telomere-to-telomere human genome reference. The new T2T Y chromosome reference has never been used before for alignment. The long read data for the Human Pangenome Project are available in PRJNA701308. The long read data for the Genome In A Bottle samples are available at: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ The combined CHM13 v1.1 + HG002 Y chromosome (CP086569.1) is temporarily available here: https://processing.open-genomes.org/reference/CP086569.1-CHM13/ Alignment of the long and short read data to the T2T reference against the new complete Y chromosome will enable us to investigate the Y phylogeny in detail using regions of the Y chromosome that were unavailable until now.