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Alignment

The ARGO Data Platform accepts raw sequencing data in both FASTQ and BAM (aligned or unaligned) format. The first processing step in the DNA-Seq Pipeline is uniformly aligning samples to the GRCh38 reference genome. For details, please see the latest version of the ARGO DNA Alignment.

Inputs

  • All alignments are performed using GRCh38 as the human reference genome
  • Submitted FASTQ or BAM files(s)

Preprocessing

  • Submitted sequencing reads (FASTQ or BAM) are converted into lane level (i.e read group level) BAMs.
  • Picard:CollectQualityYieldMetrics is used for read group level BAM QC.

Processing

Outputs

Workflow Diagram

Alignment Workflow