In order to facilitate the bioinformatics analysis of the Next Generation Sequencing (NGS) data, we regularly organize bioinformatics classes for Texas A&M faculty and students. The classes are scheduled for at least 5 interested individuals, or on a regular basis for large groups. The purpose of these classes is to provide information about NGS technology, its output data, and the available analysis tools. The class includes a demo of most popular analysis resources. If you have NGS data and would like a training session, please contact Dr. Noushin Ghaffari at firstname.lastname@example.org.
The recommended resources for analyzing the data are:
- iPlant Collaborative: a NSF founded project to support the computational and data management needs of the scientific community. iPlant is a free resource and offers different platforms and tools for variety of application, especially NGS data analysis:
- iPlant Collaborative: http://www.iplantcollaborative.org/
- iPlant learning center: http://www.iplantcollaborative.org/learning-center
- The Galaxy Services, hosted by National Center for Genome Analysis Support, is a free resource for NGS data analysis. Depending on the computational needs users can use Galaxy as an analysis tool at NCGAS at Indiana University, or apply for XSEDE allocations to receive more resources, i.e. allocations in terms of CPU, space, and memory. Different galaxy service are available at:
- Introduction to Galaxy: https://scholarworks.iu.edu/dspace/handle/2022/17204
- The High Performance Research Computing (HPRC) resources at Texas A&M University is available to TAMU students and faculty. There are different types of account types, depending on the computational needs and the applying individual.
- Here is the link to different account types provided by HPRC: https://sc.tamu.edu/wiki/index.php/HPRC:Policies:Allocations
- The Ada system in an Intel-based Linux system, and provides many bioinformatics pipeline for NGS analysis. Here is the link for Ada: https://sc.tamu.edu/wiki/index.php/Ada
- CLC Genomics Workbench: Texas A&M University owns 8 floating licenses for the CLC Genomics Workbench software suite. AgriLife Genomics and Bioinformatics group manages the users, creates accounts for TAMU affiliated individuals, and provides trainings.