Introduction

imsarath/nf-capbench is an automated and reproducible Nextflow pipeline designed to benchmark and evaluate capture kit performance. It streamlines the process of assessing sequencing data quality, coverage metrics, and enrichment efficiency, providing standardized reports for consistent comparison across samples and kits. With its modular design and containerized execution, nf-capbench ensures scalability, reproducibility, and easy integration into existing bioinformatics workflows.

1. Read QC (FastQC)
2. Adapter trimming (FastP)
3. Alignment to reference genome (BWAMEM2)
4. UMI Processing (FGBIO)
5. Post-alignment QC (Picard - CollectHsMetrics, CollectMultipleMetrics)
6. Calculate Downsampling Factors
7. Downsampling (samtools)
8. Summary Plots

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample_id,capturekit,lane,fastq_1,fastq_2
P-NA12877,ILLUMINA,L2,data/LB-P-NA12877-CFDNA-03098850-TD1-C31_S1_L002_R1_001.fastq.gz,data/LB-P-NA12877-CFDNA-03098850-TD1-C31_S1_L002_R2_001.fastq.gz
P-NA12877,ILLUMINA,L3,data/LB-P-NA12877-CFDNA-03098850-TD1-C31_S1_L003_R1_001.fastq.gz,data/LB-P-NA12877-CFDNA-03098850-TD1-C31_S1_L003_R2_001.fastq.gz
P-NA12878,EVO,L4,data/LB-P-NA12878-N-03098850-TD1-C31_S1_L004_R1_001.fastq.gz,data/LB-P-NA12878-N-03098850-TD1-C31_S1_L004_R2_001.fastq.gz
P-NA12878,EVO,L5,data/LB-P-NA12878-N-03098850-TD1-C31_S1_L005_R1_001.fastq.gz,data/LB-P-NA12878-N-03098850-TD1-C31_S1_L005_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

nextflow run imsarath/capbench \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
   --panel

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Credits

nf-core/capbench was originally written by Sarath Kumar Murugan.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #capbench channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.