MobiCT

ctDNA Analysis pipeline. Version 1.0.0

Introduction

Mobict is an analysis pipeline designed for detecting SNV and small InDels in circulating tumor DNA (ctDNA) obtained through non-invasive liquid biopsy, serving diagnostic, prognostic, and therapeutic purposes. The pipeline is built using Nextflow. The associated publication is available here: /doi/.../

Quick Start

1. Install nextflow (https://www.nextflow.io/docs/latest/install.html).

2. Create a conda environment for MobiCT:

   conda create -n MobiCT -c conda-forge -c bioconda gatk4 fgbio bwa fastp samtools picard vardict-java ensembl-vep

3. Download the reference genome

4. Download the datasets needed by VEP (see https://github.com/Ensembl/ensembl-vep)

5. Edit the .config file with input and output files/paths

6. Activate your conda environment

7. Run MobiCT on your Dataset

   Nextflow -log /output_directory/my.log run MobiCT.nf -c nextflow.config

Pipeline output

The output files are stored in the directory you specified using the outdir parameter in the .config file. The outdir contains a folder per sample plus a multiQC folder. Each sample folder contains a deduplicated and aligned .bam file and its index, an annotated .vcf file, 3 metrics files (.HsMetrics.1.txt, .HsMetrics.3.txt and QC.bcftools_stats.stats).