Prints on accordion-bound rice paper
Book of Mine project, of which Volume X is a part, presents my entire genome bases and Volume X contains the bases of one of my X chromosome. The DNA is sampled and sequenced in December 2018 and the reads were mapped to the human X chromosome reference sequence UCSC hs38. The covered bases from our sequencing were annotated as black, and uncovered bases as grey.
Collaborator: Ross McBee, Columbia University Department of Systems Biology
DNA was sampled by buccal swab with a sterile cotton tip applicator and stored on dry ice/-80 until prepped using the Qiagen DNeasy Blood and Tissue kit. A sequencing library was prepped using the Nextera DNA library prep kit and cleaned up using house-made AMPure-equivalent Serapure beads to a final average library size of ~350bp as indicated by gel. DNA was sequenced on the Illumina NextSeq 500 platform using a Mid-output 150 cycle kit with 2x84bp paired end reads, generating 130,139,348 reads passing filter. Reads were mapped to the UCSC hs38 X chromosome sequence using BowTie2, and variants were called using SAMtools/BCFtools. Bedtools was used to generate a coverage mask, and a custom python script then combined the reference chromosome, the coverage mask, and the variant file to generate the final text. Covered bases, defined as a very liberal 1x coverage depth (i.e. a single read) were annotated as black, and uncovered bases as grey. Variants with a quality <20 were not included. Heterozygous sites are shown in format [N…N/N…N]. Data was outputted as a .html file in 10megabase chunks, with per-base (or per-variant, in the case of variants) inline styling block specifying the text color, and converted to PDF format for printing using the wkhtmltopdf tool.