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Fig. 2 | BMC Infectious Diseases

Fig. 2

From: Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis

Fig. 2

Overview of the in-house pipeline. The in-house pipeline consists of a number of manual steps; input of raw data, preprocessing of paired-end (PE) FASTQ files, assembly and scaffolding followed by annotation of the assembled contigs in FASTA format. The outputs from the annotation; sequence type (MLST), virulence gene characterization (VirulenceFinder), species identification (JSpeciesWS) and presence of genes conferring antibiotic resistance (ResFinder) were manually sorted and collected into a summary (Excel-format). Circle represents data files and each box represents a component corresponding to a series of tasks that provide a certain well-defined functionality (indicated in bold). Bioinformatics tool employed in each module are also mentioned (indicated in italics)

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