Whole genome assembly of Mycobacterium canettii strains. MCANSEQ

We performed the whole-genome assembly of available sequencing read datasets (SRA Study ERP002514) from Mycobacterium canettii strains, which were isolated from patients between 1983 and 2013 mostly in the Republic of Djibouti. Illumina read pairs were first trimmed using Trimmomatic v0.36 (parameters: LEADING 20; TRAILING 20; SLIDINGWINDOW windowSize 5, requiredQuality 20; MINLEN 50; AVGQUAL 20). Complete read pairs were then assembled using SPAdes v3.10.1 (parameters: --careful; -k 21,33,55,77,99,127 according to read length; --phred-offset 33). Generated contigs were finally organized as compared to the closest reference genome of Mycobacterium canettii available (STB-A, STB-D or STB-L) using MeDuSa v1.6 (default parameters).