def _bowtie2_args_from_config(config):
    """Configurable high level options for bowtie2.
    """
    qual_format = config["algorithm"].get("quality_format", "")
    if qual_format.lower() == "illumina":
        qual_flags = ["--phred64-quals"]
    else:
        qual_flags = []
    num_cores = config["algorithm"].get("num_cores", 1)
    core_flags = ["-p", str(num_cores)] if num_cores > 1 else []
    return core_flags + qual_flags