Introduction

A bioinformatics workflow for quick assessment of illumina reads with the focus on (fastqc, species identification, coverage and estimated genome size)

Getting Started

download the project

• Set up a project folder for the run

cd /path/to/installation

• Download the latest version from gitlab

git clone https://gitlab.com/FLI_Bioinfo/qc_pipeline.git

Running the qc_pipeline

To run the qc_pipeline, run the bash script checkQC.sh. Detailed usage is below

bash ./checkQC.sh -h
USAGE:
   bash ./checkQC.sh -d fastq_directory -o Output_directory --kraken2 <path to kraken2 db>

REQUIRED:
   -d, --fastq-directory  DIR, a directory where the fastq reads are present
OPTIONAL:
   -l, --linksdir         DIR, a directory to create links for the reads (default: linksdir/)
   -o, --outdir           DIR, an output directory for the snakemake results (default: output/)
   --run [true, false]    Automatically run snakemake (default: true)
   --cores                Number of cores to use (default: available cpus) 
   --kraken2              Path to (Mini)kraken2 DB. You may download ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz
   -h, --help             This help

• As input for checkQC.sh, you need to use the folder where the fastq files are present with option -d. In standard cases, fastq files could have any of the following format (sampleID_S3_L001_R1_001.fastq.gz, sampleID_1.fastq.gz, sampleID_1.fq.gz, sampleID_1.fq .gz), could also be uncompressed.
• The script checkQC.sh creates a new folder where links for the samples are created "option -l". In this folder the name of samples is corrected to be read with snakemake in this format "sampleID_1.fastq.gz"
• Additionally, checkQC.sh writes a config file updated with paths to output folder "option -o", kraken2 DB "option --kraken2" and snakemake "default is the current folder"
• snakemake runs automatically "option --run true" with the cores "option --cores". However, the automatic run could be deactivated using --run false. In this case you need to run snakemake in a separate step.

Example

bash ./checkQC.sh -d /path/to/inputfolder -o /path/to/outputfolder --run true --cores 64 --kraken2 /home/DB_RAM/kraken2

Authors

Mostafa Abdel-Glil (mostafa.abdel-glil@fli.de)
Jörg Linde (joerg.linde@fli.de)

Contributors