CAMP: Short-Read Quality Control

Overview

This module runs a series of standard quality-control steps on metagenomic short read data. It is both self-contained (ex. instructions included for the setup of a versioned environment, etc.), and compatible with other CAMP modules (ex. ingests and spawns standardized input/output config files, etc.).

There are two filtration steps in the module- i) for general poor quality (Phred scores, length, Ns, adapters, polyG/X) and ii) for host reads- followed by a sequencing error correction step. The properties of the QC-ed FastQs are summarized in aggregate by a MultiQC report.

Approach

Installation

Clone repo from Github tutorial <https://github.com/MetaSUB-CAMP/camp_short-read-quality-control>_.
Set up the conda environment using configs/conda/short-read-quality-control.yaml.
If you don't already have Trimmomatic installed through conda or as a standalone JAR, download its precompiled binary. You'll need to update the path to said binary in the paramters.yaml file.

git clone https://github.com/usadellab/Trimmomatic.git

Make sure the installed pipeline works correctly. pytest only generates temporary outputs so no files should be created.

cd camp_short-read-quality-control
conda env create -f configs/conda/short-read-quality-control.yaml
conda activate short-read-quality-control

Download and untar the relevant databases -- make sure to update the path to these files in the parameters.yaml

wget https://s3.us-east-1.wasabisys.com/camp-databases/v0.1.1/human_genome_bt2idx/GRCh38_noalt_as.tar.gz; tar -zxvf GRCh38_noalt_as.tar.gz

Quickstart

Running each CAMP module takes the same three steps, listed below.

As with all CAMP modules, update the parameters.yaml file:

Generate your samples.csv file in the following format:

<SAMPLES.CSV FORMAT>

Deploy! ::

Module details

Input: /path/to/samples.csv provided by the user.

Output: 1) An output config file summarizing the locations of the error-corrected FastQs, 2) the MultiQC report summarizing the properties for the QC-ed FastQ, and 3) summary statistics about the dataset after each error correction step indicating how many reads and/or bases were pruned

/path/to/work/dir/short_read_qc/final_reports/samples.csv for ingestion by the next module
/path/to/work/dir/short_read_qc/final_reports/*_multiqc_report.html, where * is 'pre' or 'post'-module
/path/to/work/dir/short_read_qc/final_reports/read_stats.csv

Structure:

└── workflow
    ├── Snakefile
    ├── short-read-quality-control.py
    ├── utils.py
    └── __init__.py

workflow/short-read-quality-control.py: Click-based CLI that wraps the snakemake and unit test generation commands for clean management of parameters, resources, and environment variables.
workflow/Snakefile: The snakemake pipeline.
workflow/utils.py: Sample ingestion and work directory setup functions, and other utility functions used in the pipeline and the CLI.

Make your own samples.csv based on the template in configs/samples.csv. Sample test data can be found in test_data/.
- ingest_samples in workflow/utils.py expects Illumina reads in FastQ (may be gzipped) form and de novo assembled contigs in FastA form
- samples.csv requires either absolute paths or paths relative to the directory that the module is being run in
Download the appropriate host reference genome(s) and make a Bowtie2 index using bowtie2-build /path/to/host_reference.fa /path/to/host_reference, and add the prefix /path/to/host_reference to parameters.yaml.
Update the computational resources available to the pipeline in resources.yaml.

Command line deployment

To run CAMP on the command line, use the following, where /path/to/work/dir is replaced with the absolute path of your chosen working directory, and /path/to/samples.csv is replaced with your copy of samples.csv. - The default number of cores available to Snakemake is 1 which is enough for test data, but should probably be adjusted to 10+ for a real dataset. - Relative or absolute paths to the Snakefile and/or the working directory (if you're running elsewhere) are accepted!

python /path/to/camp_short-read-quality-control/workflow/short-read-quality-control.py -d /path/to/work/dir -s /path/to/samples.csv

Note: This setup allows the main Snakefile to live outside of the work directory.

Running on a slurm cluster

To run CAMP on a job submission cluster (for now, only Slurm is supported), use the following. - --slurm is an optional flag that submits all rules in the Snakemake pipeline as sbatch jobs. - In Slurm mode, the -c flag refers to the maximum number of sbatch jobs submitted in parallel, not the pool of cores available to run the jobs. Each job will request the number of cores specified by threads in configs/resources/slurm.yaml.

    sbatch -J jobname -o jobname.log << "EOF"
    #!/bin/bash
    python /path/to/camp_short-read-quality-control/workflow/short-read-quality-control.py --slurm \
        (-c max_number_of_parallel_jobs_submitted) \
        -d /path/to/work/dir \
        -s /path/to/samples.csv
    EOF

Quality-checking processed FastQs

To quality-check the processed FastQs, download and compare the collated MultiQC reports, which can be found at /path/to/work/dir/short_read_qc/final_reports/*_multiqc_report/html. Multiple rounds of preprocessing may be needed to fully get rid of low-quality bases, adapters, and duplicated sequences. - For example, the dataset I worked with required an additional round of fastp to trim 10 low-quality bases from the 5' and 4 low-quality bases from the 3' end respectively. - I recommend creating a new directory, which I've called /path/to/work/dir/short_read_qc/5_retrimming and placing reprocessed reads inside them. - Afterwards, I reran FastQC and MultiQC and collated summary statistics (ex. numbers of reads, etc.) from the reprocessed datasets manually. I also updated the location of the reprocessed reads in /path/to/work/dir/short_read_qc/final_reports/samples.csv to /path/to/work/dir/short_read_qc/5_retrimming.

Dependencies

Credits

This package was created with Cookiecutter <https://github.com/cookiecutter/cookiecutter>_ as a simplified version of the project template <https://github.com/audreyr/cookiecutter-pypackage>_.
Free software: MIT
Documentation: https://short-read-quality-control.readthedocs.io.

tommyfuu/camp_short-read-quality-control