SOCS

SOCS is a reference-based, ungapped alignment tool designed for mapping both standard SOLiD data and bisulfite transformed SOLiD data.

For usage instructions, see Usage.html, which is included in the package and posted in Docs and Data. Standard sample data are available at GEO, accession GSE13543. Bisulfite data will be available soon.

OS: MacOSX/Unix/Linux

SOCS was developed at the Georgia Institute of Technology and the National Biodefense Analysis & Countermeasures Center with assistance from Life Technologies.

SOCS is licensed by the GNU General Public License.

Features

Bisulfite capability	For methylation studies utilizing bisulfite sequencing, alignments can be tolerant of any bisulfite-induced nucleotide substitutions, while remaining tolerant to an additional user-specified number of color-space errors. Although runtimes will be significantly longer in this mode, it will be free of the bias caused by aligning to reference sequences with simulated conversion. See Variant mode in the Options section of Usage.html
Short variant detection	Short sequence-space variants of a user-specified length (typically 1, for SNPs) can be inferred from valid color-space variants. See Variant mode in the Options section of Usage.html
Census function	SOCS can optionally compute read coverage depth per nucleotide of the reference. Census of short variants and bisulfite transformations can also be computed.
Multiple reference files	Multiple reference files can be provided, each with multiple sequences. The files can be in FASTA or 2bit format and can be mixed in a single alignment. SOCS will find the optimal alignment for each read across all reference files provided.

Publications

Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH. Efficient mapping of ABI SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics 2008 24: 2776-2777. Full text

Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH. An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. Bioinformatics Advance Access. Full text

Contact

Please contact Nicholas Bergman, PhD at the National Biodefense Analysis & Countermeasures Center with any questions, problems, or suggestions.

bergmann@nbacc.net

Recent News
Version 2.0 Nicholas Bergman 2010-03-05 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.
Crashes with SOLiD 3 data Nicholas Bergman 2009-10-08 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.
User feedback for version 2 Nicholas Bergman 2009-04-09 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 ...
Version 1.2.1 - Important fix Nicholas Bergman 2009-01-21 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).
Version 1.2 Nicholas Bergman 2008-11-21 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.

Time	Activity Type	By
2009-Oct-09
15:53:47	Forum post: socs output to SOLiD gff v0.2? to .ma file?	Mitzi Morris

Join Project
~~Request to join project~~
Description
Alignment tool with bisulfite functionality
Developer Info
Nicholas Bergman Marc Salit
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

MyGforge Home

SOCS

SOCS

Features

Publications

Contact