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Superlink-Online SNP is a powerful tool for the analysis of snp data on large families.
The tool begins by removing erroneous and unlikely SNPs from the data. The algorithm takes into consideration both the genetic data and the capabilities of the Superlink linkage analysis software. It prepares a set of input files that can be analyzed with Superlink Online and executes them. These files can also be used later using various options of Superlink Online. Data and results are stored at a secured server in a personal account and can be removed at any time by the user.
Users can at every step easily archive all their results to a local machine to guarantee against possible data loss.
Superlink-Online SNP performs massively parallel computations using tens of thousands of CPUs.
A full description of the system is given in the following paper:
A System for Exact and Approximate Genetic Linkage Analysis of SNP Data in Large Pedigrees.
Bioinformatics (2013) 29 (2): 197-205.
A grant for a free usage of Superlink Online is provided to researchers in academic and research organizations.
User accounts and password changes are available here.
Current Superlink SNP version: 1.1
What's new in version 1.1?
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New Approximate Analasis via Morgan:
Users can perform approximate power calculation analysis using the Program Morgan marker_drop (written by Elizabeth Thompson's group).
This analysis simulates marker data at markers linked to a hypothetical trait locus, conditional on trait data and a genetic model.
This is useful for evaluating the statistical power available in a given pedigree.
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New "System Load" feature:
Indicates how many jobs are currently running in the system.
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New "Show Affection Status" option:
This option can be used in Two-point, Multi-point, Morgan lm_linkage and Morgan marker_drop analyses.
It lets the user change the affection status of every family member (healthy, affected or unknown).
This change applies to the ped file as well.
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Improved user interface:
- User can sort "Projects" table by project name, date of creation and date when last modified.
- User can no longer delete projects while they are in "running" mode.
Download Superlink
The standalone version of Superlink can be downloaded here.
Note that this version supports only exact linkage analysis. All the other features are only found in the online version.
Success Stories
Recent results using Superlink Online:
| 125. | Frank G. van Steenbeek, Bart Spee, Louis C. Penning, Anne Kummeling, Ingrid H. M. van Gils, Guy C. M. Grinwis, Dik Van Leenen, Frank C. P. Holstege, Manon Vos-Loohuis, Jan Rothuizen, Peter A. J. Leegwater.
PloS one, 8(3): e57973, 2013
| | 124. | Satya R. Vemula, Andreas Puschmann, Jianfeng Xiao, Yu Zhao, Monika Rudzi?ska, Karen P. Frei, Daniel D. Truong, Zbigniew K. Wszolek and Mark S. LeDoux.
Human Molecular Genetics, 22(12): 2510-2519, 2013
| | 123. | M. Hashim Raza, E. Michael Gertz, Jennifer Mundorff, Joseph Lukong, Judith Kuster, Alejandro A. Sch?ffer, Dennis Drayna.
Human Genetics, 132(4): 385--396, 2013
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This research is supported by Microsoft TCI grant, NIH, and the Israel Ministry of Science.
Resources are the courtesy of:
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