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. 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.
The SOLiD™ 3 System provides a comprehensive suite of commercial software. Some of the tools included in this site are available with the system as a commercial solutions. For more information about the SOLiD™ System Software please visit our website at http://www.appliedbiosystems.com/solidsoftware
Applied Biosystems SOLiD™ System Open Source Software Tools
A tool for taking the raw sequence data files from SOLiD™ SAGE™ reads and matching them to known sequences in your reference database of choice. Tool for the conversion of SOLiD output files to base sequences data with associated quality values. Tools that can be used in conjunction with publically available ChIP-seq tools such as MACS in order to identify putative binding sites and also motif finding. Tool to map transcriptome reads to a reference genome, count tags for exons and genes and view data in UCSC Genome Browser Tool to identify small indels in SOLiD™ data. Tool to identify inversions from mate-pair orientation analysis. The tools in this project provide the ability to create de novo assemblies from SOLiD™ colorspace reads.
This tool is a Genome Annotation Viewer and Editor, based on the Apollo Genome Annotation Curation Tool. SAB runs on Windows, Linux and Mac OS.
This tool enables researchers to map SOLiD color space reads to whole human genomes.
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.
This tool can be used for consolidating reference-aligned SOLiD™ data into a standard format (General Feature Format).
This tool can be used for converting native SOLiD™ data into a community-driven standard (Short Read Format) for NCBI submission.
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
This data is sample re-sequencing data from DNA originating from E.Coli DH10B. The read length of this data is 50 for each tag. These data are direct results from a quarter of a slide statistical analysis outputs from a mate-pair run. This data set was sequenced using the SOLiD™ System. It consists of a sequencing run from a fragment library of E.Coli DH10B. This data set was sequenced using the SOLiD™ System. It consists of a fragment sequencing run using a small RNA library from human samples. This data set was sequenced using the SOLiD™ System. It consists of a mRNA sequencing run using the methodology published by Cloonan, N. et al. in Nature Methods doi: 10.1038/nmeth.1223 (2008).
For questions regarding the content and information contained in the SOLiD™ Software Development Community website, please send an e-mail to SOLiDdev@appliedbiosystems.com
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