Theoretical and practical advances in genome halving

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Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “Raw sequencing reads from ChIP libraries were mapped to the human reference genome (hg19) or mouse reference genome (mm9), using bwa (72) with default parameters.”
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Population genomics of Bronze Age Eurasia (2015, background): “Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing. Cold Spring Harbor Protocols 2010, pdb.prot5448, doi:10.1101/pdb.prot5448 (2010). 40 Orlando, L.”