- Single-cell NGS automation
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- Epigenetics and small RNA sequencing
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Cogent NGS Analysis Pipeline
Now compatible with our popular bulk and plate-based RNA-seq kits!
Cogent NGS Analysis Pipeline (also referred to as CogentAP) is bioinformatic software for analyzing RNA-seq data, including gene or transcript expression counting, gene fusion detection, and immune profiling analysis. Please refer to the table at 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.
After installing, the software consists of the following features:
- CogentAP GUI launcher
- 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
Supported operating systems
CogentAP can be installed on the following versions of Linux:
- CentOS 6.9 & 6.10
- RedHat 7.5
- Ubuntu 17
For analyzing Illumina NextSeq® High-Output data:
- 24-core CPU
- 64 GB+ RAM
- 500 GB+ 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.
Additional third-party software dependencies*
- Conda (or Miniconda3)
- bcl2fastq conversion software
*Not included with the software; must be downloaded and installed separately.
Additional product information
For use in conjunction with workflows on the ICELL8 cx Single-Cell System, ICELL8 Single-Cell System, or select Takara Bio UMI kits. More information is available in the Cogent NGS Analysis Pipeline v2.0 User Manual and Quick Start Guide.
Cogent NGS Analysis Pipeline version history
|Version number||Release date||Notes|
|mappa Analyzer 1.0||2019-06-07|
Scale your biomarker discovery with full-transcriptome scRNA-seq
SMART-Seq Pro Application Kit - 2 Chip
- Capture critical insights—identify gene fusions, splice variants, and SNPs that end-counting technologies can miss
- Profile your cells with confidence—find more genes and transcripts with powerful SMART-Seq chemistry
- Prepare libraries with ease—automate your workflow from sample to library prep to analysis
- Get clear results—simplify your bioinformatics analysis with integrated Cogent NGS tools
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