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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™ 4 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 athttp://www.appliedbiosystems.com/solidsoftware
The New SOLiD™ Community Site
Created specifically for people involved in Next Generation Sequencing, the community provides a forum for meaningful discussions and interactions with other sequencing experts and SOLiD™ System users. Check out all areas of this site and let us know what you think. Discussions, blogs, polls, videos, and documents are constantly updated, so check in frequently to see what is new! Please register at http://solid.community.appliedbiosystems.com/index.jspa
Applied Biosystems SOLiD™ System Open Source Software Tools
- SOLiD™ Accuracy Enhancement Tool (SAET)
A tool that uses raw data generated by the SOLiD system to correct miscalls within reads either prior to mapping or contig assembly
- AB dibayes SNP Tool
A tool for detecting SNPs with SOliD data.
- AB Large InDel Tool
A tool for detecting large InDels in SOLiD mate pair library data.
- AB CNV Tool
A tool detecting copy number variation in human SOLiD data from fragment or mate-pair libraries.
- SOLiD™ SAGE™ Analysis Software v1.10
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.
- SOLiD™ BaseQV Tool
Tool for the conversion of SOLiD output files to base sequences data with associated quality values.
- AB ChIP-seq Accessory tools
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.
- AB WT Analysis Pipeline
Tool to map transcriptome reads to a reference genome, count tags for exons and genes and view data in UCSC Genome Browser
- AB Small InDel Tool
Tool to identify small indels in SOLiD™ data.
- AB Inversion Tool
Tool to identify inversions from mate-pair orientation analysis.
- SOLiD™ System de Novo Assembly Tools 2.0
The tools in this project provide the ability to create de novo assemblies from SOLiD™ colorspace reads.
- SOLiD™ System Alignment Browser (SAB)
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.
- 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.
- SOLiD™ DNA Methylation Analysis Tools
Here we describe a data analysis pipeline for mapping and analyzing MethylMiner™-enriched and unenriched fractions of genomic DNA as well as bisulfite-converted and unconverted reads sequenced on the SOLiD™ System.
- BioScope™ 1.3.1 Pairing Stats Tools
This script calculates pairing stats from the mapped and unmapped 1.3.1 BAM files and removes the extraneous entries from the mapped pairing BAM file. By default, it outputs a cleaned-up mapped BAM file while calculating the pairing stats.
- 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 compatibility with existing pipelines and legacy data.
Applied Biosystems SOLiD™ System Data Sets
- SOLiD™ System E. Coli DH10B Mate-Pair Data Set (2008)
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.
- SOLiD™ System E. Coli DH10B Fragment Data Set (2008)
This data set was sequenced using the SOLiD™ System. It consists of a sequencing run from a fragment library of E.Coli DH10B.
- SOLiD™ System Human Small RNA Data Set (2008)
This data set was sequenced using the SOLiD™ System. It consists of a fragment sequencing run using a small RNA library from human samples.
- SOLiD™ Whole Transcriptome Data Set(2008)
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).
- 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 toSOLiDdev@appliedbiosystems.com