Data Analysis Documentation

Bionano Solve™ is an analysis pipeline for Bionano data processing, optimized for Bionano and Saphyr Compute Servers. These tools perform computation jobs for the Saphyr.

Below are documents required for installing and interpreting the data that is produced via the analysis pipeline.
The Report Guidelines documents give guidance for interpreting QC Reports, while the Theory of Operation documents explain the fundamentals of any given analysis method. The File Format Specification Sheets give detailed explanations of the different files utilized or produced by the pipeline.

Guidelines

Data Collection - 30173, Rev E268 KB

How much data to collect for a given application.

Bionano Access Dashboard and Chip Metrics - 30304, Rev B299 KB

Interpreting the Bionano Access Dashboard view for sample quality.

Molecule Quality Report - 30223, Rev C390 KB

Interpreting the Molecule Quality Report (MQR) in Bionano access for sample quality.

De Novo Assembly Informatics Report - 30255, Rev D421 KB

Interpreting the Assembly Report from Bionano Access once the molecules have been assembled into de novo maps.

Hybrid Scaffold Report - 30324, Rev A156 KB

Interpreting the Hybrid Scaffold Report when scaffolding Bionano maps with NGS contigs.

Installation Guide

Bionano Solve Installation Guide - 30182, Rev L198 KB

Release Notes

Bionano Solve v3.7.1 Release Notes - 30456, Rev B193 KB

Specification Sheet

BNX File - 30038, Rev F367 KB
CMAP File - 30039, Rev H268 KB
XMAP File - 30040, Rev B180 KB
SMAP File - 30041, Rev H305 KB
BED File - 30164, Rev B114 KB
SVMerge File - 30165, Rev F248 KB
Hybrid Scaffold Conflict Cut Status File - 30166, Rev A123 KB
Structural Variant Annotation Pipeline File - 30168, Rev G226 KB
EnFocus FSHD Analysis JSON File - 30322, Rev B396 KB
EnFocus Fragile X Analysis JSON File - 30458, Rev A400 KB
VCF File - 30459, Rev A229 KB
Absence/Loss of Heterozygosity Pipeline File - 30460, Rev A222 KB
Copy Number Variant Annotation Pipeline File - 30461, Rev A205 KB

Theory of Operation

Structural Variant Calling - 30110, Rev L7 MB
Variant Annotation Pipeline - 30190, Rev K599 KB
EnFocus FSHD Analysis - 30321, Rev C792 KB
EnFocus Fragile X Analysis - 30457, Rev A649 KB
Hybrid Scaffolding - 30073, Rev F745 KB

User Guide

How to Align a bnx to a Reference - 30194, Rev B503 KB
Running Bionano Solve Pipeline on Command Line - 30205, Rev H383 KB

Analysis Quick Start

Analysis Quick Start: Annotated Rare Variant Calling - 30375, Rev A2 MB

Contact Support

Call 858.888.7663 or email us at support@bionanogenomics.com
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