Quickstart

Get ResistanceProfiler running in three steps.

1. Install

Install ResPro via bioconda:

conda install respro

Verify the installation:

respro --version

2. Initialize or download a database

Option A: Download a maintained database:

respro databases --list
respro databases --download db_name --output my_folder/

Option B: Create your own project database from GenBank and rules TSV files:

respro init \
    --name "My Project" \
    --genbank some_reference.gb \
    --rules rules.tsv \
    --output myrespro.db

For faster setup with less network-dependent enrichment, add --no-additional-info to skip PubChem/PubMed lookups.

See Database Preparation for metadata options and Rules TSV Format for rule file details.

3. Run profiling

Profile a FASTA consensus sequence:

respro fasta \
    --project myrespro.db \
    --fasta my_consensus_sequence.fasta \
    --output my_output \
    --results-db my_results.db \
    --export json

Or profile a VCF file with its reference FASTA:

respro vcf \
    --project myrespro.db \
    --vcf my_ngs_result.vcf \
    --ref-fasta my_vcf_ref.fasta \
    --output my_output \
    --results-db my_results.db \
    --export json

The VCF may be multi-chrom and the reference FASTA multi-record (one record per CHROM), allowing segmented viruses or multiple targets to be profiled in one run.

See CLI Reference for all commands and flags, and Output Interpretation for reading results.