Cogent™ NGS Discovery Software

Version 2.1

Overview

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

Supported applications

See a list of supported applications.

CogentDS workflows. Source data is generated by CogentAP from single-cell RNA or DNA or bulk RNA sequencing data.

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

GUI launcher (via RStudio)
Example mini-datasets

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 User Manual or Quick Start Guide.

Supported operating systems

Windows 11
macOS Mojave (v10.14) or higher
Linux CentOS 6.9+ or higher

Hardware requirements

Standard analysis
- Minimum: 8 GB RAM (Recommended: 16 GB)
- >20 GB of free disk space
Shasta Total RNA-Seq data analysis
- ≥64 GB RAM
- >60 GB of free disk space

Additional third-party software dependencies*

R
RStudio Desktop

*Not included with the software; must be downloaded and installed separately. Refer to the user manual for the complete list and more information.

Additional product information

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

Cogent NGS Discovery Software version history

Version number	Release date	Notes
CogentDS v2.1	2025-01-17	Improved, simple user interface (UI) Enhanced features for quality control and ambient RNA correction Guided end-to-end single-cell RNA (scRNA), bulk RNA, and single-cell DNA (scDNA) analysis Data discovery and analysis support for Takara Bio mRNA and total RNA-seq, Shasta Whole-Genome Amplification, and 100,000 barcodes from Shasta Total RNA-Seq kits (supported applications) Prerequisites: Requires R version 4.4 or higher Added XQuartz prerequisite for macOS support of scDNA analysis Removed requirement for R devtools
CogentDS 1.5 (re-release)	2023-05-26	New installation procedure Documentation: User Manual Quick Start Guide EULA
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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