PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution.

"the datasets are publicly available in ncbi sra repositories under the accession number prjna905805 ( methods ).; bulk rna-seq data from three species: human bonobo and chimpanzee available at sequence read archive under the bioproject prjna527986 [ ] were used to perform the comparative analyses of the transcriptomes from the phasedancer-extended subtelomeric regions.; availability of data and materials the sequence data ( fastq files) of toby and chaos chimpanzees generated for this study are available in the national center of biotechnology information (ncbi) under the sequence read archive (sra) as bioproject no prjna905805 with biosample ids samn31883988 and samn31883989 respectively and sra accession number prjna905805 [ 59 ]. all the source codes related to the article are available in github repositories and associated with doi via zenodo: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\bullet$$\end{document} ? we employed a validation pipeline commonly used to measure the quality of assemblies on such data; available at https://github com/skoren/bacvalidation [ ]. availability of data and materials section). we used the optical genomic maps generated with the nicking enzymes bsssi and bspqi of the chimpanzee and orangutan genomes from the bioproject prjna369439"

"we employed a validation pipeline commonly used to measure the quality of assemblies on such data; available at https://github com/skoren/bacvalidation [ ].; the source code the docker image of phasedancer and the toy-example along with the detailed manual are available online [ ].; the source code with the documentation is available online [ ].; the source code and the documentation of phasedancersimulator are available online [ ] t2t data of sds were used as a reference point to asses the distribution of the number of stacked sds in the human genome needed to specify the parameters for the runtime experiments.; all the source codes related to the article are available in github repositories and associated with doi via zenodo: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\bullet$$\end{document} ?"

"Declarations Ethics approval and consent to participateProcedure of collecting chimps samples was approved by the Houston Zoo Investigational Review Committee. Chimps samples were collected by Houston Zoo during routine examinations of the animals. Consent for publicationNot applicable. Competing interestsThe authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests."

"Funding The work was supported by Polish National Science Centre grant no. 2018/30/M/NZ2/00054 and 2019/33/N/ST6/03110."