1. Quick example

  1. Install ProPhyle using Bioconda:

    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda install prophyle
  2. Download the RefSeq bacterial database:

    prophyle download bacteria
  3. Build an index for randomly selected 10% genomes from the E.coli subtree (taxid 561 in the NCBI taxonomy), with k-mer size 25:

    prophyle index -s 0.10 -k 25 ~/prophyle/bacteria.nw@561 _index_ecoli
  4. Classify your reads:

    prophyle classify _index_ecoli reads.fq > result.sam