Chlamydia trachomatis Genome Sequencing

DNA was prepared for sequencing using 1 µg of input following the TruSeq DNA PCR-free protocol (Illumina, San Diego, CA). Libraries were sequenced on the Illumina MiSeq instrument as paired-end 2 × 151 base pair reads. Raw fastq reads were trimmed of adapter sequences using cutadapt version 1.12^{53 (link)} and then trimmed and filtered for quality using the FASTX-Toolkit 0.0.14 (Hannon Lab, CSHL). The remaining reads were mapped to the Chlamydia trachomatis genome (NC_000117.1, NC_017435.1) using Bowtie2 version 2.2.9^{54 (link)} with parameters –local –no-mixed -X 1000. PCR duplicates were removed using picard MarkDuplicates (Broad Institute) and variants were called using GATK HaplotypeCaller version 4.1.2.0^{55 (link)} with parameter -ploidy 1.