SOCS
SOCS uses iterative mismatch tolerances to speed up high tolerance mapping. It finds optimal alignments for each read across one or more reference files. Maps of sequence census and valid sequence-space mismatches are also provided. For repeated reference regions, all matches are recorded and their sequence census is kept separately.
OS: MacOSX/Unix/Linux
Source and MacOSX executable available in the "Files" section.
For more information and sample data, see socs.biology.gatech.edu.
| Recent News |
Crashes with SOLiD 3 data
Nicholas Bergman
2009-10-08Several users have encountered crashes that were traced to uncalled colors, which appear as "." in the csfasta file. A read filtering script has been posted with 1.2.1, and it is recommended that this script is run on any SOLiD 3 data before running SOCS.
Scripts and usage information are available in scripts.tar. |
User feedback for version 2
Nicholas Bergman
2009-04-09We are currently working on version 2 of SOCS and would like to hear how it can be improved. Let us know what kinds of features you would like to see or what kinds of bottlenecks SOCS causes in your workflow.
Here are some features we are already working on:
- bisulfite mode
- multiple contig support
- 64-bit version
To leave feedback, email socs@biology.gatech.edu or post on the thread ... |
Version 1.2.1 - Important fix
Nicholas Bergman
2009-01-21Previous versions contained a bug that affected best match files (.best.txt) for mappings that took more than one round. The read number column restarted at 0 for each round (instead of representing the absolute order in the csfasta file).
Score files (.map, .amb, .imm) were not affected.
.imm files have also been renamed to .vmm (valid mismatch). |
Version 1.2
Nicholas Bergman
2008-11-21Version 1.2 adds detection of contiguous sequence-space variants longer than 1 base (up to one less than the mismatch tolerance). Bugs reporting the number of color space mismatches for mapped reads have also been fixed. |
Version 1.1.1 problems
Nicholas Bergman
2008-11-19Version 1.1.1 has been removed because it introduced a serious bug (mapping reads that aren't matches). Our apologies for not testing it properly.
The bug it was attempting to fix will be corrected in the next version, which will be posted soon. |
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| Description |
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Color space alignment tool
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| Developer Info |
Nicholas Bergman
Marc Salit
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| Trove Categorization |
- Development Status: 5 - Production/Stable
- Intended Audience: End Users/Desktop
- License: Not Applicable
- Operating System: MacOS
- Programming Language: C++
- Spoken Language: English
- Topic: Bio-Informatics
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