def novo2(args):
    """
    %prog novo2 trimmed projectname

    Reference-free tGBS pipeline v2.
    """
    p = OptionParser(novo2.__doc__)
    p.set_fastq_names()
    p.set_align(pctid=95)
    opts, args = p.parse_args(args)

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

    trimmed, pf = args
    pctid = opts.pctid
    reads, samples = scan_read_files(trimmed, opts.names)

    # Set up directory structure
    clustdir = "uclust"
    acdir = "allele_counts"
    for d in (clustdir, acdir):
        mkdir(d)

    mm = MakeManager()
    clustfiles = []
    # Step 0 - clustering within sample
    for s in samples:
        flist = [x for x in reads if op.basename(x).split(".")[0] == s]
        outfile = s + ".P{0}.clustS".format(pctid)
        outfile = op.join(clustdir, outfile)
        cmd = "python -m jcvi.apps.uclust cluster --cpus=8"
        cmd += " {0} {1}".format(s, " ".join(flist))
        cmd += " --outdir={0}".format(clustdir)
        cmd += " --pctid={0}".format(pctid)
        mm.add(flist, outfile, cmd)
        clustfiles.append(outfile)

    # Step 1 - make consensus within sample
    allcons = []
    for s, clustfile in zip(samples, clustfiles):
        outfile = s + ".P{0}.consensus".format(pctid)
        outfile = op.join(clustdir, outfile)
        cmd = "python -m jcvi.apps.uclust consensus"
        cmd += " {0}".format(clustfile)
        mm.add(clustfile, outfile, cmd)
        allcons.append(outfile)

    # Step 2 - clustering across samples
    clustSfile = pf + ".P{0}.clustS".format(pctid)
    cmd = "python -m jcvi.apps.uclust mcluster {0}".format(" ".join(allcons))
    cmd += " --prefix={0}".format(pf)
    mm.add(allcons, clustSfile, cmd)

    # Step 3 - make consensus across samples
    locifile = pf + ".P{0}.loci".format(pctid)
    cmd = "python -m jcvi.apps.uclust mconsensus {0}".format(" ".join(allcons))
    cmd += " --prefix={0}".format(pf)
    mm.add(allcons + [clustSfile], locifile, cmd)

    mm.write()
%prog novo2 trimmed projectname

    Reference-free tGBS pipeline v2.