Introduction to Secondary pipeline

Summary of the pipeline offering

The Nostos Secondary offering provides robust alignment and variant calling solutions for germline samples, whether in singleton or trio cases. The analysis begins from FASTQ files and can be performed using either the GRCh37 or GRCh38 reference genome, based on user selection.

Key features of the pipeline include:

• Small variant detection: Using Sentieon DNAScope, the pipeline generates highly accurate small variant calls for all sample types. 
• Copy number variant (CNV) detection: For Whole Exome Sequencing (WES) or targeted panel data, ExomeDepth is used to identify CNVs in addition to small variants.
• Comprehensive quality control: The pipeline integrates quality metrics from industry-standard tools such as FastQC, Qualimap and Picard. These are compiled into a detailed MultiQC interactive HTML report, offering a clear overview of key metrics for raw reads, alignment, and variant calling. 

Minimal Input requirements

• Raw reads: Paired-end (PE) FASTQ files for each sample

Provided outputs

• Aligned reads: BAM format (available for download 1 time for each case, within 30 days of pipeline processing)
• Log2ratio bedGraph: bedGraph format
• Small variant calls: VCF format (Sentieon DNAScope)
• CNV calls (WES/Panel only): VCF format (ExomeDepth)
• Quality report: HTML format.