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| 2010-03-05 | Posted By: Nicholas Bergman Version 2.0 Version 2.0 is now available. Major updates include: - bisulfite mode - multi-sequence fasta and 2bit support - 64bit-aware A complete description of changes can be found in Version_2_guide.html under Docs and Data.  Discussions |
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| 2009-10-08 | Posted By: Nicholas Bergman Crashes with SOLiD 3 data Several 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. Discussions |
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| 2009-04-09 | Posted By: Nicholas Bergman User feedback for version 2 We 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 for this news item. Discussions |
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| 2009-01-21 | Posted By: Nicholas Bergman Version 1.2.1 - Important fix Previous 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). Discussions |
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| 2008-11-21 | Posted By: Nicholas Bergman Version 1.2 Version 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. Discussions |
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| 2008-11-19 | Posted By: Nicholas Bergman Version 1.1.1 problems Version 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. Discussions |
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| 2008-11-13 | Posted By: Nicholas Bergman Version 1.1.1 fixes Version 1.1.1 fixes the number of mismatches reported in the .best.txt file (previous versions reported the tolerance they were found at). Discussions |
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