danhumassmed/qc-tools repository overview

⁠Sofware Provided

⁠FastQC

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:

• Import of data from BAM, SAM or FastQ files (any variant)
• Providing a quick overview to tell you in which areas there may be problems
• Summary graphs and tables to quickly assess your data
• Export of results to an HTML based permanent report
• Offline operation to allow automated generation of reports without running the interactive application

⁠MultiQC

https://multiqc.info/⁠

Aggregate results from bioinformatics analyses across many samples into a single report MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

⁠RSeQC

https://pythonhosted.org/RSeQC//⁠

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

⁠Usage

The provided Docker image is compatible with Singularity⁠ and is actively used in NextFlow⁠ Pipelines configured for an HPC.

⁠Example running fastqc (Mac OSX)

local_project_dir="/Users/dan/Code/NextFlow/Bioinformatics_Training/Introduction_to_RNA-seq"
docker_project_dir="/home/rnaseq"
input_dir="raw_data"
output_dir="results/fastqc/"

mkdir -p ${local_project_dir}/${output_dir}
docker run -v ${local_project_dir}:${docker_project_dir} danhumassmed/qc-tools:1.0.1 \
    /bin/bash -c \"fastqc -o ${docker_project_dir}/${output_dir} -f fastq ${docker_project_dir}/${input_dir}/*.fq\"