Cogent™ NGS Discovery Software

Version 1.5

Overview

Cogent NGS Discovery Software v1.5 (CogentDS) is bioinformatic software for user-friendly analysis of sequencing data generated with Takara Bio platforms. The Cogent NGS Analysis Pipeline v2.0.1 (CogentAP) can be used to prepare files ready for import into CogentDS.

Top Principal Components can be reduced and visualized using the Uniform Manifold Approximation and Projection (UMAP, recommended) method or the t-Distributed Stochastic Neighbor Embedding (t-SNE) method.

Installation instructions can be found in the Cogent NGS Discovery Software v1.5 User Manual or Quick Start Guide. CogentDS includes the following files:

GUI launcher
Example mini-dataset files—can be used to test the Discovery functionality (CogentDS data object [*.rda], gene_info.csv, gm.csv, and metadata.csv)
Sample output—compare to the analysis results of the mini-dataset

Sign up to get Cogent NGS Discovery Software

If you are interested in using CogentDS, please review the End User License Agreement (EULA) before populating the required fields of the form.

After checking the box to indicate acceptance of the EULA and submitting the completed form, you will be directed to a page where you can download the software. Installation instructions can be found in the Cogent NGS Discovery Software v1.5 User Manual or Quick Start Guide.

Supported operating systems

Windows 7, Windows 10
macOS Mojave (v10.14) or higher
Linux CentOS 6.9+ or higher

Hardware requirements

8 GB RAM
>2 GB of free disk space

Additional third-party software dependencies*

R
RStudio Desktop
R devtools
Pandoc (optional; only required for advanced users that wish to forgo RStudio and run R from the command line)

*Not included with the software; must be downloaded and installed separately.

Supported applications

See a list of supported applications.

Additional product information

More information is available in the Cogent NGS Discovery Software v1.5 User Manual or Quick Start Guide.

Cogent NGS Discovery Software version history

Version number	Release date	Notes
CogentDS v2.0.14 (beta)	2024-09-30	Improved, simple user interface (UI) Enhanced features for quality control of raw sequencing data (FastQC) Guided workflows for single-cell and bulk RNA-seq analyses Enhanced features for removal of unwanted reads, like rRNA or ambient RNA Documentation: Quick Start Guide Sign up to be a beta tester here.
CogentDS 1.5 (re-release)	2023-05-26	New installation procedure
CogentDS 1.5	2021-12-03	Prerequisites: Requires R devtools 2.4.2 or later Requires R version 4.0.0 or higher New features to support extended analysis options in Cogent NGS Analysis Pipeline: Improved analysis of full-length transcriptome data: clustering by gene counts or transcript counts and transcript-count analysis reports Report overlay options for gene fusions and immune clonotypes Improved manual Quality Controls Option to select previously used analysis parameters to streamline data import and get to the reports more quickly
CogentDS 1.0	2020-09-11	Prerequisites: Requires R devtools 2.1.0 or later Requires R version 3.6.0 or higher PCA options: visualize Principal Components using either the Uniform Manifold Approximation and Projection (UMAP, recommended) or the t-Distributed Stochastic Neighbor Embedding (t-SNE) method. Documentation: User Manual Quick Start Guide EULA
hanta software 1.0	2019-06-07	Prerequisites: Requires R devtools 2.0.1 or later Requires R version 3.5.0 or higher PCA options: visualize Principal Components using the t-SNE method only. Documentation: User Guide EULA

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