Additional file 3 of In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

Additional file 3 Standardized outcomes of the cgMLST workflows BIGSdb (n = 420), INNUENDO (n = 336), GENPAT (n = 420), SeqSphere (n = 420), BioNumerics (n = 420) and MentaLiST (n = 420) applied to downsampled paired-end reads from 3 reference genomes of Listeria monocytogenes (i.e. ATCC19114, ATCC19115 and ATCCBAA679) with associated de novo assembly parameters assessed with Quast (version 5.0.2) and MultiQC (version 1.9). The targeted read depth (Dr: 10X, 20X, 30X, 40X, 50X, 60X, 70X, 80X, 90X and 100X) were prepared according to kmer depth (Dk): 8X, 15X, 23X, 30X, 38X, 45X, 52X, 60X, 67X, 75X) setting of BBNorm (read length R = 150 and kmer size K = 30). Because of internal firewall, the INNUca assembler integrated into the cgMLST workflow INNUENDO cannot not perform assemblies of paired-end reads with read depth of coverage of 20X (n = 42) and 10X (n = 42). (TSV 1207 kb)