Overview

Step up to a whole new level with the bold reinvention of genome assembly and annotation.

Presentation

Simplicity™ is NSilico's lead product and is the most comprehensive, easy-to-use, cloud-based high performance system for the automatic annotation, analysis and visualisation of genetic data.

It allows the user to perform numerous tasks such as nucleotide sequence analysis, structure fold comparison, multiple alignment, motif and domain identification, phylogenetic analysis for evolutionary relatedness, prokaryotic and viral genome analysis and gene prediction (ORF finding), gene ontology management, research workflow management and IP management with minimum effort.

Simplicity™ Video

How to submit a new assembly (step-by-step)

Trial User

On registering you will be automatically registered as trial user and will receive 50 credits to test the software. Once a user buys credits then they become a full user. These is no need to buy credits for testing.

Note

As a trial user, only 50 ORFs will be annotated for all pipelines, and contigs and scaffolds are unavailable to download, but the assembly statistics are available to view.

Simplicity™ Overview

Open a new browser tab and go to https://simplicity.nsilico.com. Below you can see the login screen. There you'll be able to either login or register (which will be necessary if it's your first time using Simplicity™).

Login Screen

Figure 1 - Login Screen

After either registering or logging in, you will be taken to the Welcome Page. Here you can create a simple pipeline. Begin by clicking the start a new pipeline link.

Available Organisms

Figure 2 - Available Organisms.

Click on the organism's button to explore the available pipelines.

Available pipelines

Figure 3 - Prokaryotic pipelines available in Simplicity™.

The available pipelines are listed. The first two pipelines analyse raw sequencing read files from Illumina.

Note

The Genome annotation of a draft genome pipeline expects a FASTA file containing either pre-assembled data (contigs) or a draft genome.

First Submission

Select the prokaryotes pipeline and then Genome annotation of a draft genome option.

Genome annotation of a draft genome form

Figure 4 - Genome annotation of a draft genome form

You can run a genome annotation pipeline by selecting My Computer and uploading a draft genome or pre-assembled FASTA file. For demonstration purposes, a preselected list of draft genomes is available (see figure 4) to choose if you do not have a genome on your computer.

When ready, press GO.

A list of completed workflows

Figure 5 - A list of completed workflows.

When the workflow has successfully started, the webpage will redirect you to the Home Page, which displays your running and completed pipelines.

By clicking on a pipeline you'll be taken to the results page for that pipeline.

Pipeline Results Page

Figure 6 - Pipeline Results Page

In the Pipeline Results Page you see a list of tools used in the pipeline. Clicking the icon for each tool will show you each tools individual settings/parameters. Clicking on the icon will display the result of the selected tool. The status bar shows the progression of each tool and also indicates the current progress status of the tool.

Submitting reads from Illumina BaseSpace®

Warning

Your current username/email must be the email address use used to register to Illimina BaseSpace® If it is not the case you can provide an alternative email address in Profile.

Login to BaseSpace®

Open a new browser tab and go to https://basespace.illumina.com/ and log-in to your Illumina BaseSpace® account.

BaseSpace® Applications

Once logged in, select App in the top menu (compass and rule icon). Then find Simplicity from the list of BaseSpace® Applications.

Simplicity App in list of BaseSpace Applicatione

Figure 7 - Simplicity App in list of BaseSpace® Application

Select the Simplicity App and click on the Launch button.

Application description page

Figure 8 - Application description page

Select your sample

You can enter a short description of your sample (optional) and select your sample read files by clicking on Select Sample(s)

Launched Application: select a sample

Figure 9 - Launched Application: select a sample

The list of all available samples will appear. Click on your sample and then select OK

Sample selection

Figure 10 - Sample selection

You are now ready to start and connect to Simplicity™ pipelines. Click on the big arrow on the right-hand side to continue.

Launched Application: ready to start

Figure 11 - Launched Application: ready to start

Permission

The first time you will start the app, you will be asked to give Simplicity™ access to your sample files. Simplicity™ needs to download to the sample read files to start the assembly and annotation process. Only the file selected will be available to Simplicity™, no other file is accessible to us. Click on the Accept button.

Grant access permission

Figure 12 - Grant access permission

Simplicity™ pipelines

You will be automatically redirected to Simplicity™ website. Your file(s) will be automatically added to the form.