Microbe-Flow is an easy to setup, modular and flexible workflow for analyzing bacterial whole genome sequencing (WGS) data. It is based on the 
platform for modular workflows design and efficient execution on computer clusters.
Microbe-Flow uses a wide range of tools to enable a comprehensive overview on large numbers of samples. It offers an automated solution for WGS, starting from FASTQ files, including raw reads quality control (QC), de novo assembly and its QC, gene prediction and annotation including virulence/resistance genes, phylogenetic analyses and typing based on variant calling and core SNPs, multilocus sequence typing (MLST) and core genome (cg)MLST.
Notably, Microbe-Flow enables a range of studies including pan-genome and association analysis for desired bacterial attributes, bi-clustering of virulence genes including enrichment and gene clusters co-localization tests. Conveniently, Microbe-Flow is not species-specific and can be adjusted to any bacterium, while species-specific steps can be added as needed. In addition, Microbe-Flow produces a detailed final report. It was designed to work hand in hand with CONDA environments, to enable an easy installation of almost all the pre-required programs and packages.
In conclusion - Microbe-Flow is well documented and has step by step walk through instructions.
