Eukaryotes Pipeline

 

eukaryotes pipeline, see text below

Eukaryotes Pipeline (Text)

  1. Read Processing
    1. Read filtering, trimming, and stats (trimmomatic + fastQC)
    2. Host/contaminant removal (Bowtie2 + BBtools)
  2. Genome reconstruction
    1. De novo assembly (SPAdes or Megahit)
    2. Eukaryote identification and validation (Tiara + metaEUK)
    3. Automated binning and dereplication (MetaBAT2 + dRep)
  3. Genomic analyses
    1. Quality estimation (BUSCO)
    2. ORF prediction (AUGUSTUS)
    3. Functional annotation (DRAM + Uniref)
    4. Abundance quantification (coverM)