Illumina Sequencing of M. tuberculosis var. tuberculosis str. S3
The NEBNext DNA Library Prep Kit (New England Biolabs) was used to generate paired-end (2x150bp) libraries before quality checking by Qubit 2.0, Agilent 2100 Bioanalyzer, and qPCR prior to WGS by Illumina NovaSeq. Novogene used proprietary software read QC, discarding paired-end reads containing contaminant adapter sequences, pairs with reads containing more than 10% uncertain nucleotide calls (N), and pairs for which a read had a phred score of less than or equal to 5.