A quality control pipeline for Oxford Nanopore sequencing

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Authors

Johannes Köster (@johanneskoester)

Usage

Step 1: Install workflow

If you simply want to use this workflow, download and extract the latest release . If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml .

Step 3: Execute workflow

Test your configuration by performing a dry-run via

snakemake -n

Execute the workflow locally via

snakemake --cores $N

using $N cores or run it in a cluster environment via

snakemake --cluster qsub --jobs 100

snakemake --drmaa --jobs 100

See the Snakemake documentation for further details.

Testing

Tests cases are in the subfolder .test . They should be executed via continuous integration with Travis CI.

Code Snippets

script:
    "../scripts/plot-signals.py"

SnakeMake From line 12 of rules/eval.smk

script:
    "../scripts/plot-read-lengths.py"

SnakeMake From line 23 of rules/eval.smk

script:
    "../scripts/plot-quals.py"

SnakeMake From line 34 of rules/eval.smk

script:
    "../scripts/plot-kmer-mapping.py"

SnakeMake From line 46 of rules/eval.smk

shell:
    "dot -Tsvg {input} "
    "-Grankdir=TB -Nshape=box -Nstyle=rounded -Nfontname=sans "
    "-Nfontsize=10 -Npenwidth=2 -Epenwidth=2 -Ecolor=grey -Nbgcolor=white " # -Ncolor='{params.color}'"
    "> {output}"

SnakeMake From line 59 of rules/eval.smk

shell:
    """
    if [ -s {input.reads} ]
    then
        kraken --threads {threads} --db {input.db} {input.reads} > {output} 2> {log}
    else
        touch {output}
    fi
    """

SnakeMake Kraken From line 12 of rules/kraken.smk

shell:
    "kraken-report --db {input.db} {input.tsv} > {output} 2> {log}"

SnakeMake From line 33 of rules/kraken.smk

script:
    "../scripts/plot-classification.py"

SnakeMake From line 45 of rules/kraken.smk

shell:
    "cat {input} | gzip > {output}"

SnakeMake From line 6 of rules/preprocess.smk

shell:
    "porechop -t {threads} -i {input} "
    "-b {params.output_dir} --format fastq.gz > {log} 2>&1; "

SnakeMake porechop From line 23 of rules/preprocess.smk

wrapper:
    "0.27.1/bio/fastqc"

SnakeMake FastQC From line 10 of rules/qc.smk

shell:
    "crimson fastqc {input} {output}"

SnakeMake FastQC CRIMSON From line 21 of rules/qc.smk

script:
    "../scripts/calc-colormap.py"

SnakeMake From line 8 of rules/utils.smk

import pickle
import common


full_tree = common.load_classification_tree(snakemake.input[0], min_percentage=0.0)
cmap = common.TreeCMap(full_tree)
with open(snakemake.output[0], "wb") as out:
    pickle.dump(cmap, out)

Python common From line 1 of scripts/calc-colormap.py

import pickle
from networkx.drawing.nx_agraph import write_dot
import common

cmap = pickle.load(open(snakemake.input.colormap, "rb"))

tree = common.load_classification_tree(snakemake.input.classification, min_percentage=1.0)
cmap.color_tree(tree)

write_dot(tree, snakemake.output[0])

Python common networkx From line 1 of scripts/plot-classification.py

import pickle
import matplotlib
matplotlib.use("agg")
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import numpy as np
import common


d = pd.read_table(snakemake.input.mapping, names=["status", "seqid", "taxid", "seqlen", "kmer_mapping"])

mappings = []
for i, per_read_mapping in enumerate(d.kmer_mapping.str.split(" ")):
    j = 0
    def mapping_stretches(row):
        global j
        taxid, count = row.split(":")
        count = int(count)
        yield from ([taxid, x] for x in range(j, j + count))
        j += count

    m = pd.DataFrame([item for row in per_read_mapping for item in mapping_stretches(row)])
    m.columns = ["taxid", "kmer"]
    m["read"] = i
    m = m.set_index(["read", "kmer"], drop=False)
    mappings.append(m)
    if i == 100:
        break

if mappings:
    mappings = pd.concat(mappings)
    mappings = mappings.taxid.unstack()
    mappings = mappings.iloc[:, :100]

    # color image in HSV representation of the circular layout of the taxid tree
    cmap = pickle.load(open(snakemake.input.colormap, "rb"))
    img = mappings.applymap(cmap.rgb)

    shape = list(img.shape) + [3]
    img = np.vstack(img.values.tolist()).reshape(shape)

    #plt.figure(figsize=(30, 10))

    plt.imshow(img, interpolation="nearest", aspect="auto")

    plt.xlabel("k-mer")
    plt.ylabel("read")

plt.savefig(snakemake.output[0])

Python Pandas numpy matplotlib seaborn common From line 1 of scripts/plot-kmer-mapping.py

import json

import pandas as pd
import matplotlib
matplotlib.use("Agg")
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np

fastqc = json.load(open(snakemake.input[0]))

qualdist = pd.DataFrame.from_records(fastqc["Per base sequence quality"]["contents"])
qualdist.Base = qualdist.Base.apply(lambda b: int(b.split("-")[0]))
qualdist = qualdist.replace("NaN", np.NaN)
single_value = qualdist["Lower Quartile"].isnull()
qualdist = qualdist[~single_value]

if not qualdist.empty:
    plt.fill_between(x=qualdist.Base, y2=qualdist["Lower Quartile"], y1=qualdist["Upper Quartile"], color="#cee3a3")
    plt.plot(qualdist.Base, qualdist.Mean, "-", color="#649600")

sns.despine()
plt.xlabel("read base")
plt.ylabel("quality (PHRED scale)")
plt.xticks(rotation="vertical")

plt.savefig(snakemake.output[0], bbox_inches="tight")

Python Pandas numpy FastQC matplotlib JSON seaborn From line 1 of scripts/plot-quals.py

import json

import pandas as pd
import matplotlib
matplotlib.use("Agg")
import seaborn as sns
import matplotlib.pyplot as plt


fastqc = json.load(open(snakemake.input[0]))

lendist = pd.DataFrame.from_records(fastqc["Sequence Length Distribution"]["contents"])
lendist["Length"] = lendist["Length"].apply(lambda l: int(l.split("-")[0]) if isinstance(l, str) else l)
total = lendist["Count"].sum()
lendist = lendist[lendist["Count"] > 1]
if not lendist.empty:
    sns.barplot(x="Length", y="Count", data=lendist, color="#649600")


sns.despine()
plt.title("total reads: {}".format(total))
plt.yscale("log")
plt.xlabel("min read length")
plt.ylabel("count")
plt.xticks(rotation="vertical")

plt.savefig(snakemake.output[0], bbox_inches="tight")

Python Pandas FastQC matplotlib JSON seaborn From line 1 of scripts/plot-read-lengths.py

import json

import pandas as pd
import matplotlib
matplotlib.use("Agg")
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
import h5py


def get_signals():
    for f in snakemake.input:
        f = h5py.File(f, "r")
        for read, group in f["Raw"]["Reads"].items():
            yield group["Signal"]


for signal in get_signals():
    l, u = snakemake.params.steps
    signal = signal[l:u]
    plt.plot(np.arange(signal.shape[0]), signal, "-", color="#649600")


sns.despine()
plt.xlabel("")
plt.ylabel("raw signal")
plt.xticks([])

plt.savefig(snakemake.output[0], bbox_inches="tight")

Python Pandas numpy matplotlib JSON seaborn h5py From line 1 of scripts/plot-signals.py

shell:
    "snakemake --nolock {input} --report {output}"

SnakeMake Snakemake From line 34 of master/Snakefile

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


from os import path
from tempfile import TemporaryDirectory

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

def basename_without_ext(file_path):
    """Returns basename of file path, without the file extension."""

    base = path.basename(file_path)

    split_ind = 2 if base.endswith(".gz") else 1
    base = ".".join(base.split(".")[:-split_ind])

    return base


# Run fastqc, since there can be race conditions if multiple jobs 
# use the same fastqc dir, we create a temp dir.
with TemporaryDirectory() as tempdir:
    shell("fastqc {snakemake.params} --quiet "
          "--outdir {tempdir} {snakemake.input[0]}"
          " {log}")

    # Move outputs into proper position.
    output_base = basename_without_ext(snakemake.input[0])
    html_path = path.join(tempdir, output_base + "_fastqc.html")
    zip_path = path.join(tempdir, output_base + "_fastqc.zip")

    if snakemake.output.html != html_path:
        shell("mv {html_path} {snakemake.output.html}")

    if snakemake.output.zip != zip_path:
        shell("mv {zip_path} {snakemake.output.zip}")