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For account activation and project access, or for questions regarding the content and information contained in the SOLiD™ Software Development Community website, please send an e-mail to SOLiDdev@appliedbiosystems.com

SOLiD™ Software Development Community

The SOLiD™ Software Development Community Program supports life scientists and independent software vendors in the development and potential commercialization of bioinformatics applications for next-generation DNA sequencing platforms.  Applied Biosystems has expanded its Software Development Community to include sample data sets and open-source software tools for the SOLiD™ System. The goal of this program is to directly address the challenges associated with analyzing and managing the vast amounts of research data generated by this ultra-high-throughput sequencing technology.

Created specifically for people involved in Next Generation Sequencing, the community provides a forum for discussions and interactions with other sequencing experts and SOLiD™ System users.

Please register at http://solid.community.appliedbiosystems.com/index.jspa

Applied Biosystems SOLiD™ System Open Source Software Tools   

• Extensible Sequence (XSQ) File Format and Tools

This describes a new open standard data output file format which is the touchpoint between the 5500 Series SOLiD Sequencing System and the LifeScope 2 Analysis Suite, including support for the Exact Call Chemistry (ECC) Module. Some of its other benefits are i) much smaller file sizes for faster processing, ii) hierarchical structure for more granular access to data and metadata, and iii) XSQ Tools to facilitate compatiblity with existing pipelines and legacy data.

• HAPS Tools

This software tool is a hybrid assembly tool. You can use Ion Torrent long reads for assembly and SOLiD Mate pair read data to create scaffold.  

Applied Biosystems 5500 Genetic Analyzer Data Sets

• 5500 HuRef Mate-paired Data Set (2011)

Human genomic DNA (HuRef) mate-paired library sequenced on the 5500xl Genetic Analyzer to 60 bp for each tag (2 x 60).

• 5500 Whole Transcriptome Paired-end Data Set (2011)
  

Whole transcriptome, paired-end (75 x 35) sequence data generated on the 5500xl Genetic Analyzer.   

Applied Biosystems SOLiD™ System Data Sets

• SOLiD™ System E.Coli DH10B 50X50 Mate-Pair Data Set (2010)
  

This is a 50X50 Mate pair library from DH10B produced by SOLiD™ system.

• SOLiD™ 4 System E. Coli DH10B Fragment Data Set (2010)

These data are sample re-sequencing data from DNA originating from E.Coli DH10B. The read length is 50 bp.

• SOLiD™ System E. Coli DH10B Bisulfite Converted Data Set (2010)

Bisulfite converted (gel and solution) data in support of Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, et al. (2010) Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding. PLoS ONE 5(2): e9320.

• SOLiD™ System Targeted Resequencing data set for barcoded samples enriched with Agilent SureSelect 38MB Human All Exon Kit (2010)

This dataset is sample targeted resequencing exome data that was generated from the SOLiD™ 3 plus System after preparing samples with Agilent™ SureSelect enrichment method.

• Whole Transcriptome Paired-End Data Set (2010)

This data set was generated by sequencing SOLiD™ Total RNA-Seq prepared libraries using paired-end reads of 50bp (forward) and 25 bp (reverse) on the SOLiD™ 4 System. 

For questions regarding the content and information contained in the SOLiD™ Software Development Community website, please send an e-mail to SOLiDdev@appliedbiosystems.com