CLI Reference

usage: eris -i genome.gfa -d targets.fasta [options]

Graph-aware contextual annotation of targeted genomic features

📁:
  Input arguments

  -i , --genome         Path to a genome in fasta or GFA format; File may be
                        compressed. (default: None)
  -d , --targets        Path to target nucleotide features in fasta or mmi
                        format (default: None)

💾:
  Output arguments

  -o , --outprefix      Prefix for output files (if absent, prints TSV to
                        stdout) (default: None)
  --no-gff              Do not write GFF3 output for global genes (default:
                        False)
  --no-faa              Do not write FAA output for global proteins (default:
                        False)

⚙️:
  Pipeline arguments

  --hops                Maximum number of contextual genes to sweep
                        upstream/downstream (default: 3)
  -l , --tolerance      Distance tolerance (bp) for merging clustered target
                        alignments (default: 0)
  -t , --max-workers    Maximum number of worker threads for alignment and CDS
                        prediction (default: None)

🎯:
  Target arguments

  -f , --feature-type   Type of feature to annotate (default: CDS)
  --indexing-threads    Number of threads to use for indexing if not already
                        indexed (default: 3)

🛠️:
  Other options

  -q, --quiet           Suppress console logging output (default: False)
  -v, --version         Show version number and exit
  -h, --help            Show this help message and exit