Cogent™ NGS Analysis Pipeline and Cogent NGS Discovery Software now in beta

Cogent AP v3.0.19 (beta) and Cogent DS v2.0.14 (beta)

Become a beta tester today to experience new data analysis features.

We’ve been working on something exciting! Try our newest update to the Cogent NGS Analysis Pipeline (CogentAP) and Cogent NGS Discovery Software (CogentDS) bioinformatics tools. CogentAP will take your raw sequencing data and create reports ready to import into CogentDS, which will visualize your data by generating enlightening figures. As next-generation sequencing (NGS) becomes increasingly time- and cost-efficient, your research will produce more data than ever before. Make sure your software is optimized to analyze these increasingly complex datasets by updating today.

In the new beta versions of both CogentAP and CogentDS you will find enhanced features for:

Quality control of raw sequencing data (FastQC)
Removal of unwanted reads, like rRNA or ambient RNA

In the new CogentAP beta you will find:

Simplified single-command installation
Streamlined demultiplexing of high-throughput NGS datasets
Enhanced features for analysis of Unique Molecular Identifiers (UMIs)
Enhanced features for accurate gene and transcript counting
Seamless integration with Nextflow for greater scalability and cloud compatibility

In the new CogentDS beta you will find:

Improved, simple user interface (UI)
Guided workflows for single-cell and bulk RNA-seq analyses

Sign up to be a beta tester

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

After checking both boxes to indicate acceptance of the CogentAP EULA and the CogentDS EULA and submitting the completed form, your browser will be directed to a page where you can download the software. Installation instructions can be found in the CogentAP v3.0.19(beta) Quick Start Guide and the CogentDS v2.0.14(beta) Quick Start Guide.

We would like to hear from you. Please send your feedback about this new beta release to technical_support@takarabio.com.

Installation details

	CogentAP v3.0.19 (beta)	CogentDS v2.0.14 (beta)
Supported operating systems	CogentAP can be installed on the following versions of Linux: CentOS 8 or higher Red Hat 8 or higher Ubuntu 18.04 or higher	Windows 11 macOS Mojave (v10.14) or higher Linux CentOS 6.9 / Red Hat 7 or higher
Hardware requirements	CPU: 24 cores Memory: 64 GB RAM Free disk space: at least 500 GB	Memory: 8 GB RAM or higher Free disk space: at least 2 GB
Additional third-party software dependencies*	Conda 24.4.0 or higher Bash UNIX shell *Not included with the software; must be downloaded and installed separately.	R version 4.4.0 or higher and: For Windows: RTools 4.4 or higher, based on the R version For MacOS: Homebrew; after R installation, please install Xcode tools and run brew install libomp and brew install gcc Linux (CentOS): use yum install to install libomp-devel and gcc RStudio (IDE for R) Pandoc *Not included with the software; must be downloaded and installed separately.
Supported applications	See a list of supported applications.	See a list of supported applications.
Additional product information	Required input files: FASTQ files generated by an Illumina^® sequencing platform An well-list text file, Illumina sample sheet, or similar TDT/CSV file	Required input files: CogentDS.analysis.rds, an rds file output from Cogent NGS Analysis Pipeline (CogentAP v3.0.19 (beta))—recommended input for full analysis capabilities .rda file format, including backward compatibility with .rda file from CogentAP v2.0.1. Please note that certain functionalities may be limited when using .rda file from a previous version of CogentAP. Raw gene-count matrix and stats/metadata files (.csv/.csv.gz )

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