Cogent™ NGS Analysis Pipeline and Cogent NGS Discovery Software beta download

Thank you for your interest in becoming a beta tester!

Download the software

CogentAP:
- Input your raw sequencing data and:
  - For customers using Shasta chemistries (Shasta WGA and Shasta Total RNA-Seq), CogentAP will demultiplex your sequencing data into individual FASTQ files.
  - For customers using our plate-based SMART-Seq kits, CogentAP will demultiplex your sequencing data and perform adapter trimming, alignment, and gene and/or transcript counting to generate reports and output files ready for visualization in CogentDS.
CogentDS:
- Visualize your data by generating figures from the reports produced by CogentAP

NOTE: If you are interested in CogentDS, please make sure you download and install CogentAP first.

Click on the icon to download each installation ZIP file.

CogentAP v3.0.19 (beta) installation ZIP file for all operating systems

Please refer to the CogentAP Quick Start Guide to install the software.

CogentDS v2.0.14 (beta) installation ZIP file for all operating systems

Please refer to the CogentDS Quick Start Guide to install the software.

NOTE: A persistent internet connection is required during installation.

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 ICELL8^® 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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