Targeted sequencing alignment workflow

Snakemake workflow for processing targeted paired-end Illumina sequencing data.

Configuration

1. Download the workflow: git clone https://github.com/morinlab/targeted_seq_alignment_workflow.
2. Edit the sample file under config/samplelist.tsv with your samples of interest.

• This will be a 3-column config file containing sample_id, path_to_R1_fastq, path_to_R2_fastq.
• Use "#" to comment out lines.

3. Edit the workflow config file under config/cappseq_normal_config.yaml for your project's parameters.
4. Create a conda environment containing snakemake version 7 or newer, and activate that environment.
5. Run the workflow using snakemake --use-conda -c <number_of_threads>

Workflow

This workflow performs the following steps:

1. Processes FASTQ files using FASTP to remove trailing Illumina adapters and sequencer-specific artifacts.
2. Align reads against the reference genome using BWA.
3. Mark duplicate reads using Picard MarkDuplicates.

The following Quality Control metrics are calculated:

• Duplicate rate (Picard MarkDuplicates).
• Capture efficiency (Picard CollectHsMetrics).
• Target-region coverage (Picard CollectHsMetrics).
• Oxidative artifacts (Picard CollectOxoGMetrics).
• Fragment size (Picard CollectInsertSizeMetrics).
• General read/contamination metrics (FASTQC).

Results

• Final processed BAM files can be found under 99-final/.
• Final QC report can be found under Q9-multiqc.