Use Sra Toolkit
The Sequence Read Archive (SRA Toolkit) stores raw sequence data from 'next-generation' sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.
- How To Use Sra Toolkit
- See Full List On Osc.edu
- Sratoolkit - How To Use SRA Toolkit To Blast SRA Accessions ...
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Availability and Restrictions
The following versions of SRA Toolkit are available on OSC clusters:
| Version | Owens | Pitzer |
|---|---|---|
| 2.6.3 | X | |
| 2.9.0 | X | |
| 2.9.1 | X | |
| 2.9.6 | X* | X* |
| 2.10.7 | X | X |
You can use module spider sratoolkit to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access
How To Use Sra Toolkit
SRA Toolkit is available to all OSC users. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
National Center for Biotechnology Information, Freeware
Usage
Usage on Pitzer and Owens
Set-up
module load sratoolkit. The default version will be loaded. To select a particular SRA Toolkit version, use module load sratoolkit/version. For example, use module load sratoolkit/2.9.6 to load SRA Toolkit 2.9.6Download SRA Data
The issue has been reported here.
You can download SRA data to local directory with prefetch
The default download path is in your home directory ~/ncbi/public. For example, you can find the SRA file SRR390728.sra in ~/ncbi/public/sra and the resource files in ~/ncbi/public/refseq. Use srapath to check if the SRA accession is available in the download path
Now you can run other SRA tools, e.g. fastq-dump on computing nodes. Here is a job script example:
However, our Home Directory file system is not suitable for heavy computation. If the SRA file is large, you can consider the following options for better performance.
Change default download path to a faster file system, i.e. /fs/scratch
You can change the default download path for SRA data to our scratch file system with one of following two approaches. For example, /fs/scratch/PAS1234/johndoe/ncbi:
Your SRA data would be stored in /fs/scratch/PAS1234/johndoe/ncbi
Further Reading
The Health Insurance Portability and Accountability Act (HIPAA) Security Rule requires that covered entities and its business associates conduct a risk assessment of their healthcare organization. A risk assessment helps your organization ensure it is compliant with HIPAA’s administrative, physical, and technical safeguards. A risk assessment also helps reveal areas where your organization’s protected health information (PHI) could be at risk. To learn more about the assessment process and how it benefits your organization, visit the Office for Civil Rights' official guidance.
What is the Security Risk Assessment Tool (SRA Tool)?
The Office of the National Coordinator for Health Information Technology (ONC), in collaboration with the HHS Office for Civil Rights (OCR), developed a downloadable Security Risk Assessment (SRA) Tool to help guide you through the process. The tool is designed to help healthcare providers conduct a security risk assessment as required by the HIPAA Security Rule and the Centers for Medicare and Medicaid Service (CMS) Electronic Health Record (EHR) Incentive Program.
All information entered into the SRA Tool is stored locally to the users’ computer or tablet. HHS does not receive, collect, view, store or transmit any information entered in the SRA Tool. The results of the assessment are displayed in a report which can be used to determine risks in policies, processes and systems and methods to mitigate weaknesses are provided as the user is performing the assessment. The target audience of this tool is medium and small providers; thus, use of this tool may not be appropriate for larger organizations.
The updated version of the popular Security Risk Assessment (SRA) Tool was released in October 2018 to make it easier to use and apply more broadly to the risks of the confidentiality, integrity, and availability of health information. The tool diagrams HIPAA Security Rule safeguards and provides enhanced functionality to document how your organization implements safeguards to mitigate, or plans to mitigate, identified risks. The new SRA Tool is available for Windows computers and laptops.
The tool is now more user friendly, with helpful new features like:
- Enhanced user interface
- Modular workflow
- Custom assessment logic
- Progress tracker
- Threats & vulnerabilities rating
- Detailed reports
- Business associate and asset tracking
- Overall improvement of the user experience
For details on how to use the tool, download the SRA Tool 3.2 User Guide [PDF - 4.8 MB].
See Full List On Osc.edu
Legacy Version: Security Risk Assessment Tool Version 2.0
Still using the old version of the tool? Note that you can’t directly transfer data from 2.0 to 3.0, but can upload certain portions (e.g., lists of assets and BAs). Refer to the SRA Tool User Guide 2.0 [PDF - 4.5 MB]* for more information.
Paper-based version of the SRA 2.0 tool is also available:
*Persons using assistive technology may not be able to fully access information in this file. For assistance, contact ONC at PrivacyAndSecurity@hhs.gov
The Security Risk Assessment Tool at HealthIT.gov is provided for informational purposes only. Use of this tool is neither required by nor guarantees compliance with federal, state or local laws. Please note that the information presented may not be applicable or appropriate for all health care providers and organizations. The Security Risk Assessment Tool is not intended to be an exhaustive or definitive source on safeguarding health information from privacy and security risks. For more information about the HIPAA Privacy and Security Rules, please visit the HHS Office for Civil Rights Health Information Privacy website.
Sratoolkit - How To Use SRA Toolkit To Blast SRA Accessions ...
NOTE: The NIST Standards provided in this tool are for informational purposes only as they may reflect current best practices in information technology and are not required for compliance with the HIPAA Security Rule’s requirements for risk assessment and risk management. This tool is not intended to serve as legal advice or as recommendations based on a provider or professional’s specific circumstances. We encourage providers, and professionals to seek expert advice when evaluating the use of this tool.