Prokaryotes Pipeline

 

Prokaryotes pipeline see text below

Prokaryotes Workflow (text)

  1. Read Processing
    • Read filtering, trimming, and stats (trimmomatic + fastQC)
    • Contaminant removal / Subsampling (Bowtie2 + BBtools)
  2. Metagenome-Assembled Genome (MAG) reconstruction
    • De novo assembly, and stats (SPAdes or Megahit, QUAST)
    • Automated binning and refinement (MetaBAT2, MaxBin2, CONCOCT, metaWRAP)
    • Dereplication (dRep)
  3. MAG analyses
    • Quality estimation (CheckM)
    • Taxonomic placement (GTDB-tk)
    • Functional annotation (DRAM)
    • Abundance quantification (coverM)