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