1. Clindet

1.1. Introduction

Clindet is a next-generation high-throughput sequencing data analysis workflow designed for clinical applications (e.g., DNA-seq, RNA-seq).
Clindet is a Snakemake pipeline for comprehensive analysis of cancer genomes and transcriptomes, integrating multiple state-of-the-art tools to generate consensus results. The pipeline supports a wide range of experimental setups, including:

• FASTQ input files

• Whole genome sequencing (WGS), whole transcriptome sequencing (WTS), and targeted/panel sequencing

• Paired tumor/normal and tumor-only sample configurations

• Most GRCh37 and GRCh38 reference genome builds

• Non-human species (e.g., mouse, worm)

1.2. Pipeline overview

1.3. Steps

• Quality Control: (Conpair, fastp)

• Read alignment: (BWA-MEM2 (DNA), STAR (RNA))

• Read post-processing: (GATK MarkDuplicates , GATK BaseRecalibrator , GATK ApplyBQSR)

• SNV, MNV, INDEL calling: (SAGE, HaplotypeCaller, Mutect2, Strelka, CaVEMan, Varscan, Muse, Pindel )

• SV calling: ( BRASS, Manta, Delly, svaba, gridss )

• CNV calling: (AMBER, COBALT, PURPLE, ASCAT, free-C, Battebberg, sequenza, Facets, ExomeDepth)

• SV and driver event interpretation: LINX

• RNA transcript analysis: (RSEM,Salmon,kallisto)

• RNA fusion gene detection: Arriba

• Summary report: ORANGE,Rmarkdown

1.4. Compare to other tools

1.5. Usage

Note

If you are new to snakemake, please refer to this page on how to set-up snakemake. Make sure to test your setup before running the workflow on actual data.

Note

It is recommended to create a Snakemake file for each project. Specific examples can be found in the Clindet directory, including template/snake_wes.smk, template/snake_wgs.smk, and template/snake_rna.smk. Project-specific parameters can be modified within these files.

Detail See Setup Clindet

1.6. Book structure

1. Part 1 (Quick overview) brief introduction of ClinDet.

2. Part 2 (Workflows Details) Usage details of ClinDet.

3. Part 3 (usecase) show some real world applications of ClinDet.

1.7. Credits

The ClinDet pipeline was written and is maintained by Yuliang Zhang (@Yuliang Zhang) , Junyi Zhang and Jianfeng Li from the National Research Center for Translational Medicine at Shanghai.

We thank the following organisations and people for their extensive assistance in the development of this pipeline, listed in alphabetical order:

• Broad Institute

• German Cancer Research Center

• Hartwig Medical Foundation Australia

• Wellcome Sanger Institute

• New York Genome Center

• JianFeng Li

• JunYi Zhang

1.8. Want to help?

If you find any bugs or want to have a new feature, please file an issue. Feel free to contact me.