======================================================================= Viromics conda environment cheat sheet Activate the right environment for each task, then deactivate. ======================================================================= TASK ENVIRONMENT KEY TOOLS ----------------------------------------------------------------------- QC / trimming / utilities viromics-core fastqc, multiqc, fastp, seqkit, prodigal, cd-hit, bowtie2, samtools, coverm, mafft, iqtree De novo assembly viromics-core megahit, metaspades, quast Viral identification virsorter2 virsorter run ... Viral identification genomad genomad end-to-end ... Score-based (optional) virfinder Rscript run_virfinder.R Score-based (optional) deepvirfinder dvf.py Quality assessment checkv checkv end_to_end ... Dereplication (vOTUs) vclust vclust prefilter/align/cluster Taxonomy network vcontact2 vcontact2 ... Phage taxonomy (optional) phabox phabox --task end_to_end Functional annotation eggnog emapper.py ... Viral functions / AMGs vibrant VIBRANT_run.py ... Viral functions / AMGs dramv DRAM-v.py annotate/distill Host prediction iphop iphop predict ... Host prediction (optional) wish WIsH -c build/predict ----------------------------------------------------------------------- Quick commands ----------------------------------------------------------------------- conda activate viromics-core # switch on an environment conda deactivate # switch it off conda env list # list all environments conda run -n virsorter2 # run one command in an env, no activate =======================================================================