This page lists frequently asked questions for Geneious Biologics, organised by section. If you have encountered an error or job failure that you would like us to help you with, see this article to find out how to send a job error report to our support team.

You can also find our video tutorial series on Getting Started with Geneious Biologics here. The first one is embedded below:

Jump to:

• General
• Accounts and Users
• Data and Integration
• Pre-processing
• Antibody Annotation and analysis
• Viewing your Annotation results
• Post-annotation analysis
• Reference Databases
• Collections
  
  

General

How do I create a folder?

Hover over the top-level folder you would like to create a new folder under - three dots should appear. Click these three dots and select New Folder. Type in the name of this new folder and press enter.

Can I manage the sharing of my folders?

Yes, Geneious Biologics allows you to manage the permissions of your folders and documents, facilitating sharing folders with other users in your organisation. Click on the three dots of any folder to manage sharing:

How do I upload files and what file types does Biologics support?

Files can be imported by either dragging and dropping files from another application (like Geneious Prime) or using the Upload button to select files on your computer. To see what file types we support, see Supported file types for Import/Export. To troubleshoot problems with uploading see this article.

How do I move files to a different folder?

Selected files can be moved to a different folder using the Move button. See this article for more information.

How do I save experiment information?

You can add info to folders within your organization. This information is useful for searching for a specific experiment and also keeping track of experiments, as it can be queried through the global  Files and Folders search.

How do I submit feedback for job failures?

To receive support on an unexpected job failure, you can report a bug directly within the Geneious Biologics application.

How do I cite Geneious Biologics in a research paper?

To cite Geneious Biologics in your paper, please use the following in the Methods section:

(Geneious Biologics 20XX*. (https://www.geneious.com/biopharma))

*Where 20XX is the year.

Accounts and Users

How do I get access to Geneious Biologics?

See this article if you are having trouble activating your Biologics account.

How do I reset my password?

See this article if you would like to reset your Biologics password.

What is the difference between administrator accounts and non-administrator accounts?

This article outlines the permissions/features that are available to administrators only.

 

Data and Integration

What browsers are supported?

We primarily support Chrome, however Microsoft Edge Chromium works for many users. To find out more, see here.

Is there a REST API available?

Yes, Geneious Biologics has a secure RESTful API available for customers to utilise for the purposes of workflow automation and integration. To access the latest documentation for the API, please see this article. To create API keys to use with the API, please see our guide here. 

What file types are supported for Import/Export?

To find out what file types you can upload and export, see Supported file types for Import/Export.

Can I use Geneious Prime together with Geneious Biologics?

We do have a plugin for Prime that allows you to synchronise Geneious Biologics and Geneious Prime, however it is in early-release form. Please see this article for more information.

Pre-processing

How do I group standalone sequences?

The Group Sequences pre-processing step is useful if you have a large amount of sequences that you would like to group into a single list.

How do I rename a large number of sequences or documents?

The Batch Rename pre-processing step is used to add or remove parts from the names of your sequences. This can make for easier sorting and processing further downstream. 

What is a Name Scheme and why is it useful for analysing Sanger sequences?

A Name Scheme can be used if you have a uniform naming convention across your sequences. For example: VH_Donor1_rev.ab1. You can use the "parts" of the name to assign specific data to the sequence such as the chain type or sample. These "parts" can be used to tell Biologics how to designate and handle your sequences in downstream analysis once assigned - for example pairing chains.

How do I set paired reads?

To find out how to set paired reads while not merging them, see this article. This may be used in cases where not all read pairs are expected to overlap but you would like to retain this sequence information.

How do I merge paired reads?

Find out how to merge paired sequences produced by various NGS sequencing technologies in this article.

How do I merge overlapping fragments of a DNA sequence into a longer contig?

Batch Assemble Sanger Sequences is useful for when you are working with Sanger sequences that form overlapping reads of your sequences.

How do I find and call heterozygous bases?

You can use the Find Heterozygotes pipeline either before (Sanger sequences only) or after assembling reads. It is also available as an option when running the Batch Assemble Sanger Sequences operation.

How can I process Barcoded data/data with UMIs?

Find out how our platform handles your Barcoded sequences using the Collapse UMI Duplicates & Separate Barcodes pre-processing step. To learn more about what Barcodes and UMIs are, see Understanding Single Cell technologies: Barcodes and UMIs. If you would like to learn more about different Single Clone/Cell workflows, see this article.

Sequence Annotation

Can I save the settings I use for analysis?

Yes, you can create shareable Profiles to save all the settings used for all our annotation pipelines.

Can my Organization standardize the settings for analysis?

Yes, you can create shareable Profiles to save all the settings used for all our annotation pipelines.
 

Can I adjust my CDR definitions?

Yes, you can change or add offsets for when you want different regions to start or end. This article outlines the three ways you can do this.

Can my sequences be numbered according to different numbering schemes?

Yes, see this article to find out more about the numbering schemes we support.

How do I annotate and view germline gene differences?

This is an option you can turn on in all our Annotation pipelines. Sequence variants relative to the reference database used will appear as annotations on your sequences, and will be listed in the sequences table. To learn more, see this article.

Can I annotate chimeric sequences, and track which species contributed the V, D or J Gene?
Yes, you can select multiple different Reference Databases when running an annotation, such as the Human Ig and Mouse Ig databases. This will track which database/species each gene was extracted from.

What are antibody sequence liabilities and can I specify liabilities of my own?

Liabilities include probable sequencing errors or protein sequence motifs that may reduce the conformational stability/otherwise impair the functioning of antibody products. Liabilities show up as annotations on your sequences; see this article to learn more about them. You can also specify your own sequence liabilities using this guide.

What is a "cluster"?

"Clusters" is a term used to refer to when sequences in a dataset are grouped together based on their sequence identity/similarity across a specific region. To learn more about clusters and how to find clusters in your dataset, see this article.

How do I add additional annotations for the constant region/signal peptides/fusion proteins to my sequences?

There are two ways to do this. You can make your own Feature Database to find and annotate larger sequences, this works best for fusion proteins or portions of the constant region. Smaller tags are best added as Assets which you can specify under Liabilities and Assets.

Viewing your Annotation results

How can I investigate the quality of my dataset?

The graphs tab which is available when viewing any Biologics Annotator Result document can be useful for quality control. The Pipeline Report tab also contains info relevant to quality control, like the Mutation distribution by gene plot.

Can I add assay data to my analysis results?

Yes, you can import assay data from excel/.csv files. To find out how to do this, see this article.

How do I filter my results?

The filter search bar is very flexible and can be used to pull out sequences that meet a specified criteria - including assay data results if assay data has been added. To find out how to use the filter search bar see this article.

What is a clonotype and how can I find them in my data?

Geneious Biologics automatically generates a number of graphs to help you to interpret your sequences and find broader trends or discrepancies in your dataset: Using graphs to interpret clusters and clonotypes. You may want to specify your clonotype as a "cluster": Clustering Options. To find out more about what a clonotype is, see this article.

What are labels and how do I add them to my sequences?

Labels can be created by all users and are used to "tag" sequences of interest. These labels may serve as a company wide identification system of potential candidates for downstream analysis.

How do I rearrange/hide columns from the Sequences Table?

Columns can be dragged to re-arrange the order, and the Table Preferences pop-out can be used to search for and hide/show columns of interest. Learn more about Table Preferences and how to save custom column preferences as "Profiles" in this article.

How do I search for a CDR3 region across experiments?

The Global search function allows users to search for Files and Folders, or CDR3 regions across all data from multiple experiments within an organization.

Can I change the color of my nucleotide and amino acid sequences?

Yes, there are a number of presets available. To learn more see this article.

How do I view and extract annotated sequences?

You can export any number of sequences as a .geneious file or export sequence tables as .csv files. To find out how, see this article. You can also use Extract and Recluster to re-analyse a subset of your sequences.

Post-annotation analysis

How do I align sequences?

You can align sequences using the Align... operation under Post-processing options. Aligning sequences is a good way of visually comparing sequences, and can include a tree, assay data, and cluster information.

How do I compare results from multiple experiments?

You can select multiple Biologics Annotator Result Documents and then run the Compare Results operation under Post-processing options. To learn more about what Compare Results does, see this article.

How do I repair low quality sequences after annotation?

You can use the Repair Sequences pipeline to salvage poor sequences that are otherwise difficult to compare against your high quality sequences due to sequencing errors or missing data. To learn more about how Repair Sequences works, see this article. Note: this is an alpha feature in active development.

How do I find common occurring motifs in my sequences?

You can use the Discover Motifs operation under the Post-Processing options to identify conserved and commonly occurring amino acid motifs or amino acid properties in your sequences. Note: this is an alpha feature in active development.

Reference Databases

What are reference databases?

A reference sequence database is a collection of already annotated sequences that can be used as a reference to annotate query sequences. To learn more about what reference databases are, see this article. The reference databases supplied by Geneious Biologics comprise the known germline gene sequences for various species. 

Can I use custom sequences sequences as my reference database?

Yes, you can. This resource details how you can create your own reference databases (both target sequences and germline gene sequences) to annotate your dataset with.

Can I create Primer sets?

Yes, see this page to find out how.

Collections

What is a collection?

Collections are a way of saving curated lists of annotated antibody sequences, complete with assay data and other relevant sequence information. To find out more see this article.

How do I create a collection?

You can follow this guide to make a Collections folder. This resource outlines the various ways you can save or add sequences to a collection.

How do I search against a collection?

This article explains how Collections can be searched against to find any sequences that are closely related to your selected candidates.