10x Genomics
GemCode Genome & Exome

Long Ranger1.3, printed on 11/22/2024

What is Loupe?

Loupe is a genome browser designed to visualize the Linked-Read data produced by the 10x GemCode Platform. Loupe is named for a jeweler's loupe, which is used to inspect gems.

Loupe is a desktop application for Windows, Mac, and Linux. It loads the .loupe files produced by the Long Ranger pipeline. Its features include:

• Summary View
  At-a-glance dashboard summarizing performance of the sequencing run and the GemCode partitioning and barcoding process.

• Haplotype Browser
  A genome browser that shows how the GemCode linked-read data resolves called SNPs, indels, and structural variants onto multi-megabase phase blocks.

• Structural Variants
  Visualization of the barcode overlap evidence for the large-scale structural variants called by Long Ranger.

• Linked-Reads
  Low-level visualization of the underlying barcoded, linked-read data and the long template molecules from which they originated.