Data and code availability
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There are three separate sequencing data sets: Short read data for two parental samples, short read data for the progeny samples and Hifi sequencing data for the parental samples. All three data sets have been uploaded on NCBI database as SRA. Accession numbers are listed in the key resources table.
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All algorithms are implemented as part of the WhatsHap phasing suite (Patterson et al., 2015). The status of all original code by the time the experiments were run has been deposited at Zenodo and is publicly available as of the date of publication. Instructions how to run this code have been included. Existing software, which is either directly used by the phasing algorithm or contributed significantly to the data procession are Hifiasm, Snakemake and PuLP. A reference to these tools is listed in the key resources table.
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Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. Except for read mapping and initial variant calling, all experiments have been run through a snakemake pipeline, which has been deposited at Zenodo. In order to enable access to the input VCF files for the novel phasing algorithm, we separately uploaded this processed intermediary files under a separate DOI on Zenodo, which is listed in the key resources table.