Cogent NGS Analysis Pipeline download

Version 3.3

Thank you for your interest in the Cogent™ NGS Analysis Pipeline!

Download the software

Click on the icon to download the CogentAP install package.

Linux, CentOS, Ubuntu, RedHat (64-bit versions)

Please refer to the installation directions in the User Manual or Quick Start Guide to install the software.

Supported operating systems

CogentAP can be installed on the following versions of Linux:

• CentOS 8 or higher
• RedHat 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® outputs may be possible on servers with less computational power than the specifications above. Analysis of HiSeq® or NovaSeq™ outputs 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.