Melange configuration

To adapt Melange to your needs, change the default parameters in the configuration file config.yaml:

Input

By default, Melange looks for the input files in the ‘example_data’ directory. You can either change these definitions or transfer your data to this folder (delete example data so that it doesn’t appear in the final output).

# --- Input
inputdir: "example_data"

Melange can accept three file formats: Fasta nucleotide files, Fasta amino acid files and Fastq files. To be recognisable by Melange, make sure the following extensions are correct or change them accordingly:

  nucleotide_extension: "{genome}.fa"
  aminoacid_extension: "{genome}.faa" 
  fastq_extension: "{genome}.fastq"

Finally, specify what kind of files Melange should start with.

  file_type: "nucleotide" # OPTIONS: "nucleotide" "aminoacid" "fastq"

Output

Directories where your output files will appear.

outdir: "results" 
outdir_anno: "results/Annotation" 

Predefined expectation value thresholds. Only change this if you have a specific rationale behind this decision.

# --- Evalues:
cog_evalue: "1e-5" #for rpsblast
pfam_evalue: "1e-5" #for hmmsearch
merops_evalue: "1e-5" #for blastp