Getting Started with Geneious Biologics

The Getting Started video series guides new Geneious Biologics users through account activation, platform navigation, and file upload, then Sanger and NGS sequence pre-processing, antibody annotation with the Antibody Annotator, cluster and graph interpretation, bioassay data integration, sequence alignment, and exporting results. The series spans ten videos, each 1 to 3 minutes.

Course Content

Set Up Your Account

Activate your Geneious Biologics organization, then add users and assign admin privileges from the Administration tab. Set up name schemes, custom reference databases, and labels before you start annotating.
LENGTH 2 minutes

A Brief Tour of the Interface

Navigate the Geneious Biologics folder tree, sequence table, and sequence viewer, then create, share, and permission folders by experiment. Upload FASTA, FASTQ, GenBank, ab1, CSV, and Excel files by drag-and-drop or the Upload button.
LENGTH 2 minutes

Pre-Process Sanger Sequences

Trim low-quality ends from Sanger sequences using the default 0.05 error probability, then batch assemble forward and reverse reads into contigs matched by file name. Pair heavy and light chains automatically using Name Schemes.
LENGTH 3 minutes

Pre-Process NGS Sequences

Pair and merge forward and reverse NGS reads, such as Illumina MiSeq data, using BBMerge within Geneious Biologics. Separate barcoded sequences and collapse UMI duplicates to assign reads to cells or wells and screen out probable sequencing errors.
LENGTH 3 minutes

Annotate Antibody Sequences

Annotate antibody sequences, including chains, scFv, and Fab, against a reference database using the Antibody Annotator. Identify germline gene differences and liabilities, then define clusters by identity, such as 85% CDR3 similarity for clonotypes.
LENGTH 2 minutes

Interpret Graphs and Clusters

Review the pipeline report for annotation rates, cluster diversity, gene association, and mutation rates against the reference database. In the Graphs tab, visualize top clonotype counts, V and J gene combination frequency, and CDR3 length distribution.
LENGTH 2 minutes

Interpret Results in Data Tables

Customize the Sequence Table by toggling, reordering, and saving column layouts as profiles, then view translation, liability, and germline annotation tracks in the Sequence Viewer. Layer filters by quality or cluster identity to refine results.
LENGTH 2 minutes

Add Bioassay Data to Sequences

Import bioassay data from Excel or CSV and match it to sequences by a shared column, combining it with annotation and liability data for candidate selection. Filter on the new assay columns, such as melting temperature, or use labels to tag sequences.
LENGTH 2 minutes

Align Antibody Sequences

Align annotated and filtered antibody sequences by region, choosing amino acid or nucleotide alignment and from several alignment and tree-building algorithms. Visualize the resulting tree alongside bioassay data to compare similarity at key regions.
LENGTH 1 minute

Export and Extract Sequences

Export filtered sequences as sequence files or Excel metadata, or extract them to a new document that preserves annotations. Export the lowest-liability sequence per cluster, and download graphs and the pipeline report as images, CSV, or PDF.
LENGTH 3 minute

Common Questions About Geneious Biologics

What is Geneious Biologics?

Geneious Biologics is cloud-based software for antibody discovery and engineering that analyzes antibody sequence data to identify, optimize, and prioritize therapeutic candidates. It supports Sanger, NGS, and single-cell datasets and annotates antibody types including mAb, Fab, scFv, VHH, TCR, and VH/VL pairs in a single collaborative workspace.

How does the Antibody Annotator work in Geneious Biologics?

The Antibody Annotator assigns CDR/FR regions from germline or custom databases, identifies germline gene differences, and flags sequence liabilities. Results are clustered by sequence identity and displayed in an interactive table with filterable columns, graphs, and alignment views.

What does the Getting Started with Geneious Biologics video series cover?

The series covers ten short videos spanning the full initial workflow: account activation and user management, platform navigation and file upload, Sanger and NGS sequence pre-processing, antibody annotation, results interpretation in graphs and data tables, adding bioassay data, sequence alignment, and exporting data.

Can I integrate bioassay data with sequence analysis in Geneious Biologics?

Yes. Bioassay data can be imported from Excel or CSV files and merged with annotated sequences. Once integrated, assay values are searchable and filterable alongside sequence properties, and can be visualized in alignments and cluster graphs to support candidate prioritization.

What sequence data types does Geneious Biologics support?

Geneious Biologics accepts Sanger, NGS, and single-cell antibody sequence datasets. Files can be uploaded by drag-and-drop or via the Upload button, and the platform includes pre-processing pipelines for paired-end merging, batch Sanger assembly, barcode separation, and UMI deduplication.

How is data shared and kept secure in Geneious Biologics?

Geneious Biologics is a cloud-based platform with folder-level sharing and permission controls. Organizations can collaborate in a shared workspace, and the platform holds ISO 27001:2022 certification for information security management.

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