Pathogen: clinical or host-associated sample from Chlamydia trachomatis
SureSelectXT Target Enrichment employed an upgraded RNA bait library consisting of 35,996, 120-mer probes spanning 86 GenBank Ct reference and clinical chromosomes and plasmids (Agilent Technologies, INC, Santa Clara, CA, reference: ELID: 3325141). Capture libraries were sequenced as 150 bp paired end reads on an Illumina NovaSeq instrument for at least 100x coverage per genome (~1.05 Mb Ct genome; ~7 kb plasmid).