Whole genome assembly of two Mycobacterium africanum strains. MAFSEQ

We performed whole-genome assembly of the two following strains of the mycobacterium tuberculosis complex: (1) Mycobacterium africanum 01 (lineage L6); and (2) Mycobacterium africanum 65 (lineage L5.1). Genome sequencing was performed at the Biomics platform of the Institut Pasteur (Paris, France) using a HiSeq 2500 device. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 28; TRAILING 28; SLIDINGWINDOW windowSize 5, requiredQuality 28; MINLEN 50; AVGQUAL 28). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful; -k 21,33,55; --phred-offset 33). Generated contigs were finally organized as compared to the reference genome of Mycobacterium africanum GM041182 using MeDuSa v1.6 (default parameters).