dsDNA Virus Pipeline

 

DsDNA pipeline, see text below

 

DsDNA viruses pipeline (text)

  1. Read Processing
    1. Read filtering, trimming, and stats (trimmomatic + fastQC)
    2. Contaminant removal / Subsampling (Bowtie2 + BBtools)
  2. Viral genome reconstruction
    1. De novo assembly and stats (SPAdes or Megahit, QUAST)
    2. Virus identification (Virsorter2, geNomad and VIBRANT)
    3. Virus ID QC and representative clustering (checkV)
  3. VOTU analyses
    1. Quality estimation (checkV)
    2. Taxonomic inference (vConTACT3)
    3. Functional annotation (DRAMv)
    4. Abundance quantification (coverM)
    5. Host prediction (iPHOP)