title: WGS of MC2-155: delta BioA-Msmeg3196
design: Methods: Between 100 and 120ng of genomic DNA was sheared by Covaris and WGS libraries were prepared using the KAPA Hyper Kit (Roche). PCR amplification of the libraries was carried out for 8 cycles. 5M PE75x2 reads were obtained for each sample on an Illumina MiSeq sequencer. Post-run demultiplexing and adapter removal were performed and fastq files were inspected using TrimGalore (Krueger, F. (2012). Trim Galore: a wrapper tool around Cutadapt and FastQC. Avaliable at: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Trimmed fastq files were then aligned to the reference genome (M. smegmatis str. MC2-155; NCBI Reference Sequence: NC_008596.1) using bwa mem (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60). Bam files were sorted and merged using samtools (Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9.). Read groups were added and bam files de-duplicated using Picard tools and GATK best-practices were followed for SNP and indel detection (A framework for variation discovery and genotyping using next-generation DNA sequencing dataDePristo M, Banks E, Poplin R, Garimella K, Maguire J, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly M, 2011 NATURE GENETICS 43:491-498).