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Bioinformatics Software: CLC Genomics Workbench

USC CLCBio License

The Norris Medical Library has licensed the CLC Genomics Workbench (CLC Gx) for the free use of USC faculty, students and staff. 

Number of Concurrent License Seat at USC

 CLC Genomics Workbench

2

 CLC Microbial Genomics Module

1

 CLC Genome Finishing Module

1

Rules on Access Session Limit

 

Maximum Single Session Duration

Maximum Number of Sessions

Analysis Examples Fitting Within the Session Limit

Peak Hours

9 am to 5 pm, Monday-Friday

4 hour

ONE

Miscellaneous analysis on small dataset; check results; generate graphs

Weekday Off Peak Hours

20 hour

(from 1 pm to 9 am the next weekday)

UNLIMITED

Various NGS workflow on small dataset < 20GB

(raw reads only allowed for miRNA-seq and Bisulfite-seq)

Weekend and Holiday

68 hour

(from 1 pm Friday to 9 am the following Monday)

UNLIMITED

Various NGS workflows on datasets < 100GB; Metagenomics; De novo genome assembly

Note: If you need to use CLC Gx longer than the maximum session limits, you must first request a special permission.

Users who violate any of the rules stated below will be warned in writing. Three such violations will result in a 12-month suspension of the offender’s access privilege of this software.

Important usage rules for everyone

Each Time You Use the Software 

  1. If you have installed Microbial Genomics and/or Genome Finishing Module in your CLC Gx, make sure both modules are disabled unless you will be using them for that particular session.  Failure to disable the modules means your continuing occupying a license seat for the modules, thus preventing other users from accessing them. (See screenshot below)
  2. You must close the software after each use, failure to exit the software means your continuing occupying a license seat, thus preventing other users from using the software. 

Disable Genome Finishing Module and/or Microbial Genomics Module each time you use the software

Rules on Analyzing Large Dataset (total raw dataset exceeds 100GB)

You must first request a special permission before analyzing a large dataset (>100GB) in CLC Gx.

Rules on RNA-seq Data Analysis

  1. In principle, RNA-seq analysis is not allowed in CLC Gx IF the total size of the dataset exceeds 20 GB (.fastq.gz files).  Instead, you are strongly encouraged to take advantage of a powerful and speedy end-to-end RNA-seq workflow in Partek Flow.
  2. If you absolutely need to use CLC’s RNA-seq tool, and your dataset size is less than 20 GB, you can only run the analysis either during the weekday off-peak hours (maximum session duration is 20 hours, starting at 1 pm and ends at 9 am the following day), or over weekends.
  3. If your RNA-seq dataset is great than 20 GB but less than 100 GB (fastq.gz files), you can only use the software over weekends and holidays (maximum session duration is 68 hours, starting at 1 pm on Friday and ending on 9 am the following Monday).
  4. Small RNA-seq analysis is allowed in CLC Gx.

 

Rules on DNA-seq or ChIP-seq Data Analysis.

  1. In principle, you can only use aligned reads as the input for DNA-seq or ChIP-seq data analyses in CLC Gx. 
  2. With several popular aligners, Partek Flow is a much faster and user-friendly solution for aligning raw sequencing reads.
  3. If you absolutely need to use CLC’s proprietary aligner, and your dataset size is less than 20 GB, you can only run the analysis either during the weekday off-peak hours (maximum session duration is 20 hours, starting at 1 pm and ends at 9 am the following day), or over weekends.
  4. If your dataset size is greater than 20 GB but less than 100 GB, you can only run the analysis over weekends (maximum session duration is 68 hours, starting at 1 pm on Friday and ending on 9 am the following Monday).