6. Example Workflows with SPUMONI

Overview

This page shows some example workflows to show how you would run spumoni in different scenarios.

Scenario 1:

• Using a single FASTA file, applying minimizer digestion, and classifying using matching statistics

./spumoni build -r ecoli_genome.fa -o index/ecoli_index -m -M
./spumoni run -r index/ecoli_index -p reads.fa -m -M

Scenario 2:

• Using a single FASTA file, not using minimizer digestion, and classifying with pseudo-matching lengths and writing to report.

./spumoni build -r ecoli_genome.fa -o index/ecoli_index -P -n
./spumoni run -r index/ecoli_index -p reads.fa -P -c -n 

Scenario 3:

• Using a list of FASTA files, using minimizer digestion, performing multi-class classification using matching statistics, and writing to report.

./spumoni build -i file_list.txt -o index/complete_index -M -m
./spumoni run -r index/complete_index -p reads.fa -d -M -c -m

Scenario 4:

• Using a list of FASTA files, not using minimizer digestion, performing multi-class classification using pseudo-matching lengths, and writing to report.

./spumoni build -i file_list.txt -o index/complete_index -P -n
./spumoni run -r index/complete_index -p reads.fa -d -P -c -n