graph TD
A[Raw data]-->B[Cleaning of low quality reads and human reads: cutadapt, sickle, bwa mem]
A-->C[Quality control: FastQC and MultiQC]
B-->C[Quality control: FastQC and MultiQC]
B-->D[Taxonomic classification of reads: Kaiju]
B-->E[Assembly: MetaSPAdes or Megahit]
E-->F[Annotation: Prokka]
F-->G[Clustering: cd-hit]
G-->H[Quantification of reads for each gene cluster in each sample: featureCounts]