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INDUCE-seq® Analysis User Guide

Pipeline v2.1  |  Doc Rev #004  |  Effective Date: May 2026

For use with: BreakMap Solution

1.0 Introduction

INDUCE-seq Analysis, enabled by LatchBio, is a web-based platform for identifying and visualising DNA breaks captured during the On-Demand INDUCE-seq Solution Workflow. The platform processes sequencing data into actionable insights delivered as HTML output reports.

This user guide provides detailed instructions for performing the INDUCE-seq Analysis workflow, including starting an analysis run, navigating the BSB INDUCE-seq Analysis Workspace, and understanding the generated output reports.

Note

For information on preparing next-generation sequencing (NGS) libraries using the On-Demand INDUCE-seq Solution assay, refer to the On-Demand INDUCE-seq Solution Assay User Guide.

What INDUCE-seq Analysis does

The pipeline performs the following operations in sequence:

  1. Quality trimming and filtering of sequencing reads from the On-Demand INDUCE-seq Solution assay.
  2. Read mapping to the specified reference genome, converting mapped reads into the genomic coordinates corresponding to the DNA breaks from which each read was derived.
  3. Break merging and counting — adjacent breaks are merged to group those forming part of the same break site.
  4. Ranking and annotation of cumulative breaks by recurrency, with intersection against in silico-predicted off-target sites, genes, and repeat regions.
  5. Aggregation of all annotated breaks into a comprehensive set of homology- and frequency-based sites for downstream review and analysis.

1.1 Workflow Overview

The diagram below summarises the end-to-end INDUCE-seq Analysis workflow.

INDUCE-seq Analysis Workflow overview diagram

Step Action
1 INDUCE-seq sequencing run complete
2 Convert BCL to FASTQ
3 Gather analysis input information (sample sheet, guide sequences, sequencing data, QC metrics)
4 Sign in to LatchBio
5 Access BSB INDUCE-seq Analysis Workspace
6 Import data
7 Manage data registry
8 Connect sequencing data
9 Run INDUCE-seq Analysis Workflow

Documentation notices

The information in this guide is proprietary to Broken String Biosciences and may be updated at any time without prior notice. This documentation is for Research Use Only and is not intended for use in diagnostic procedures.

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