Cogent™ NGS Analysis Pipeline

Version 3.1

Overview

Cogent NGS Analysis Pipeline (also referred to as CogentAP) is bioinformatic software for analyzing single-cell RNA-seq, bulk RNA-seq, and single-cell DNA-seq data. Functionalities include gene or transcript expression counting, in silico ribodepletion, gene fusion detection, immune profiling analysis, and more. Please refer to the table in the bioinformatics resource portal for the full list of validated Takara Bio reagent kits supported for use with the pipeline. CogentAP inputs raw sequencing data and outputs an HTML report and other files, such as a gene matrix, to continue further analysis. Output also includes R data objects, which may be used as input for Cogent NGS Discovery Software.

Install the software to access the following features:

Command-line interface program
Mini-dataset files (WellList.txt and FASTQ files)—used to test the CogentAP functionality
Sample output reports and stats—used to compare to the analysis results of the mini-dataset test

Sign up to get the Cogent NGS Analysis Pipeline

If you are interested in using CogentAP, 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, your browser will be directed to a page where you can download the software. Installation instructions can be found in Cogent NGS Analysis Pipeline User Manual or Quick Start Guide.

Supported operating systems

CogentAP can be installed on the following versions of Linux:

CentOS 8 or higher
Red Hat 8 or higher
Ubuntu 18.4 or higher

Hardware requirements

For analyzing Illumina NextSeq® High-Output data:

24-core CPU
64 GB+ RAM
1 TB available hard drive space*

Analyzing MiniSeq® or MiSeq® data may be possible on servers with less computational power than the specifications above. Analysis of HiSeq® or NovaSeq™ data would require better hardware than is listed.

*Data generated using the Shasta Total RNA-Seq Kit or Shasta Whole-Genome Amplification Kit requires at least six times the size of the input FASTQ files of free hard drive space for analyses with default parameters, and at least ten times the size of the input FASTQ files of free hard drive space for analyses including ribodepletion, immune profiling, and fusion analyses.

Additional third-party software dependencies*

Conda
bcl2fastq or BCL Convert for conversation of sequencer FASTQ output files

*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 Analysis Pipeline User Manual or Quick Start Guide.

Cogent NGS Analysis Pipeline version history

Version number	Release date	Notes
CogentAP v3.1	2025-01-15	Changes to install and upgrade procedure New pipeline framework (Nextflow) New DNA-seq analysis workflow, including CNV calling with Ginkgo New DNA-seq demux option Option to perform ribodepletion of data using SortMeRNA New kit data input options: Shasta Total RNA-Seq Kit and the Shasta Whole-Genome Amplification Kit
CogentAP v3.0.19 (beta)	2024-09-30	Improved, easy single-command installation Streamlined demultiplexing of high-throughput NGS datasets Enhanced features for quality control of raw sequencing data (FastQC) Enhanced features for unique Molecular Identifiers (UMI) analysis Enhanced features for accurate gene and transcript counting Enhanced features for removal of unwanted reads, like rRNA or ambient RNA Seamless integration with Nextflow for greater scalability and cloud compatibility Documentation: Quick Start Guide
CogentAP 2.0.1	2023-05-26	Updated launch procedure Documentation: User Manual Quick Start Guide
CogentAP 2.0	2022-08-17	New plate-based kit data input option: SMART-Seq mRNA LP (with UMIs), SMART-Seq mRNA, and SMART-Seq mRNA LP (refer to the bioinformatics resources portal for a full list of supported kits) Documentation: User Manual Quick Start Guide
CogentAP 1.5.1	2022-03-25	New plate-based kit data input options Adds Nextera®- and TruSeq®-based adapter sequences for trimming New default gene fusion analysis filtering level to improve identification of true fusions New variable to customize filtering levels for gene fusion analysis (CLI-only) Minor bug fixes Documentation: User Manual Quick Start Guide
CogentAP 1.5	2021-12-03	Prerequisites: Requires Miniconda3 version 4.10.2 or higher Improved support for full-length transcriptomics, with additional options for transcript, gene fusion, and immune profiling analysis New kit data input options: SMART-Seq Pro Application Kit - 2 Chip Documentation: User Manual Quick Start Guide
CogentAP 1.0	2020-09-11	Prerequisites: Requires Miniconda3 version 4.8.2 or higher Requires bcl2fastq New kit data input options: ICELL8 Single-Cell System 3' DE for UMI workflow, SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (includes UMIs) Documentation: User Manual Quick Start Guide
mappa Analyzer 1.0	2019-06-07	Prerequisites: Requires Miniconda3 version 4.5.0 or later Kit data input options: ICELL8 system sequencing results of full-length transcriptome or single-cell differential expression (3' DE or 5' DE) workflows, no UMI support Documentation: User Guide

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