def tophat(args):
    """
    %prog tophat folder reference

    Run tophat on a folder of reads.
    """
    from jcvi.apps.bowtie import check_index
    from jcvi.formats.fastq import guessoffset

    p = OptionParser(tophat.__doc__)
    p.add_option("--gtf", help="Reference annotation [default: %default]")
    p.add_option("--single", default=False, action="store_true",
                 help="Single end mapping")
    p.add_option("--intron", default=15000, type="int",
                 help="Max intron size [default: %default]")
    p.add_option("--dist", default=-50, type="int",
                 help="Mate inner distance [default: %default]")
    p.add_option("--stdev", default=50, type="int",
                 help="Mate standard deviation [default: %default]")
    p.set_phred()
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    num = 1 if opts.single else 2
    folder, reference = args
    reference = check_index(reference)
    for p, prefix in iter_project(folder, n=num):
        outdir = "{0}_tophat".format(prefix)
        outfile = op.join(outdir, "accepted_hits.bam")
        if op.exists(outfile):
            logging.debug("File `{0}` found. Skipping.".format(outfile))
            continue

        cmd = "tophat -p {0}".format(opts.cpus)
        if opts.gtf:
            cmd += " -G {0}".format(opts.gtf)
        cmd += " -o {0}".format(outdir)

        if num == 1:  # Single-end
            a, = p
        else:  # Paired-end
            a, b = p
            cmd += " --max-intron-length {0}".format(opts.intron)
            cmd += " --mate-inner-dist {0}".format(opts.dist)
            cmd += " --mate-std-dev {0}".format(opts.stdev)

        phred = opts.phred or str(guessoffset([a]))
        if phred == "64":
            cmd += " --phred64-quals"
        cmd += " {0} {1}".format(reference, " ".join(p))

        sh(cmd)
%prog tophat folder reference

    Run tophat on a folder of reads.