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Applied Biosystems 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. As part of this initiative, Applied Biosystems has expanded its Software Development Community to include new 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.

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Applied Biosystems SOLiD™ System Open Source Software Tools (unsupported)

• SOLiD™ System Color Space Mapping Tool (mapreads)

This tool enables researchers to map SOLiD color space reads to whole human genomes.

• SOLiD™ System Analysis Pipeline Tool (Corona Lite)
  

This tool can be used to map color space reads to large or small genomes, to place and annotate paired reads, and to call SNPs.

• SOLiD™ System GFF Conversion Tool (matoGff)
  

This tool can be used for consolidating reference-aligned SOLiD™ data into a standard format (General Feature Format).

• SOLiD™ System SRF Conversion Tool (solid2srf)
  

This tool can be used for converting native SOLiD™ data into a community-driven standard (Short Read Format) for NCBI submission.

• SOLiD™ System Small RNA Analysis Tool (rna2map)
  

This tool is a small RNA SOLiD™ System Analysis Pipeline for human whole genome alignment of small RNA sequencing data with tag counting features.

Applied Biosystems SOLiD™ System Data Sets

• SOLiD™ System E. Coli DH10B Mate-Pair Data Set

This data set was sequenced using the SOLiD™ System.  It consists of a subset of a sequence run from a mate-pair library and represents 293 panels of data or 1/8 of a slide totaling 58 million reads.  It is approximately a 100X coverage of the E. Coli DH10B genome.

• SOLiD™ System E. Coli DH10B Fragment Data Set
  

This data set was sequenced using the SOLiD™ System.  It consists of a sequencing run from a fragment library of E.Coli DH10B.

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