pipeline-resources

About Aladdin Genomics pipeline

Aladdin Genomics is a Nextflow analysis pipeline designed to detect germline or somatic variants from whole genome or targeted sequencing data. The pipeline was originally adapted from nf-core/sarek, a workflow designed to detect variants in whole genome or targeted sequencing data. It focuses on human reference genomes and can handle tumor/normal pairs, as well as additional relapses. Please find the sample report here

Source of the pipeline

This pipeline was originally adapted from the community-developed nf-core/sarek pipeline version 3.2.3. Zymo Research made significant contributions to the adaptation effort. These contributions mainly include modifications of variant callers used for somatic and germline samples, the integration of nf-pcgr, and improvements to the report and its documentation.

What is in the pipeline

This pipeline is built using Nextflow. A brief summary of pipeline:

Depending on the options and samples provided, the pipeline can currently perform the following:

• Form consensus reads from UMI sequences (fgbio)
• Sequencing quality control and trimming (FastQC, fastp)
• Map Reads to Reference (BWA-mem2)
• Process BAM file (GATK MarkDuplicates, GATK BaseRecalibrator, GATK ApplyBQSR)
• Summarise alignment statistics (samtools stats, mosdepth)

• Variant caller:

  • main_caller: Activate the main variant caller. If set to germline, DeepVariant is used to detect germline variants, applicable only for normal samples (status 0 in metadata.csv). If set to somatic, Mutect2 is used to detect somatic variants, applicable only for tumor samples (status 1). If no Panel of Normals (PON) is provided, the default GATK PON is used.
  • structural_caller: Activate Manta to detect structural variants.
  • copy_number_caller: Activate CNVkit to detect copy number variations.
  • msi_caller : Activate MSIsensorpro to assess microsatellite instability (MSI) using paired tumor-normal samples (defined by status in ‘metadata.csv’).
• Variant filtering and annotation (Ensembl VEP)
• Categorize Single Nucleotide Variants (SNVs) and Insertions/Deletions (InDels) detected in somatic (PCGR) and germline samples (CPSR)
• Summarise and represent QC (MultiQC)

For details, please find the source code here.

Citations

Garcia M, Juhos S, Larsson M et al. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved] F1000Research 2020, 9:63 doi: 10.12688/f1000research.16665.2.

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.