Software Community: Data Analysis Resources for Scientists
& Developers

Are you a life scientist interested in applications to analyze and manage the vast amounts of data generated by the SOLiD™ System? Are you an independent software vendor or academic researcher interested in developing software for next-generation sequencing? In this site, you will find resources to help, including:

Academic and open-source software
Commercial software
Sample data sets
Technical documentation
Data conversion tools

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Data Analysis Software, Data Sets, and More

Application-Specific Software

Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

ChIP-Seq File Formating Tool
Enables you to convert result files generated by aligning SOLiD reads to reference sequences using SOLiD software into a format compatible with most available ChIP-seq analysis tools. Available as source code.

MACS
Enables you to convert result files generated by aligning SOLiD reads to reference sequences using SOLiD software into a format compatible with most available ChIP-seq analysis tools. Available as source code.

QuEST
A Kernel Density Estimator-based package for analyzing massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).

Gene Expression

SOLiD™ SAGE™ Analysis Software
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.

De Novo Sequencing

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.

Velvet
De novo of short reads (EMBL-EBI)

ADIR
ADiR is an assembler for AB SOLiD™ colorspace reads that makes use of color transition properties in resolving overlap and consensus.

De Novo Accessory Tools

Resequencing

SOLiD™ System Analysis Pipeline Tool
Allows you to map color space reads to large or small genomes, to place and annotate paired reads, and to call SNPs. Available as source code.

AB Small InDel Tool
This stand-alone tool enables you to find small indels in SOLiD™ data.

AB Inversion Tool
This stand-alone tool enables you to detect inversions in SOLiD™ data.

AB Large InDel Tool
This stand-alone tool enables you to find large indels in SOLiD™ data.

AB CNV Tool
This tool is designed to detect copy number variation using SOLiD™ data from a single human sample mapped to the human reference sequence.

AB SNP Finder Tool (diBayes)
The diBayes package is the tool to identify SNPs from mapped and processed SOLiD™ System color space reads.

CNV-seq
CNV-seq is a new method to detect DNA copy number variation (CNV) using high-throughput sequencing. This method was published in BMC Bioinformatics 2009, 10:80.

Small RNA Analysis

Small RNA Analysis Pipeline Tool
A small RNA SOLiD™ System Analysis Pipeline for human whole genome alignment of small RNA sequencing data with tag counting features. Available as source code.

Whole Transcriptome Analysis

AB WT Analysis Pipeline
Allows you to align transcriptome reads to a reference genome, tag counting for exons and genes, and output data in base space.

RNA-MATE
A computational pipeline which provides automatic and integrated way to align color- space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context.

General Software (for Multiple Applications)

Data Analysis Tools

Galaxy
Galaxy allows you to analyze multiple alignments, compare genomic annotations, profile metagenomic samples, and much much more—without the need to install or download anything. For developers, it is an open-source, scalable framework for tool and data integration.

Data Conversion Tools

General Feature Format (GFF) Conversion Tool
Enables you to consolidate reference-aligned SOLiD™ data into a standard format (General Feature Format). Available as source code.

Sequence Read Format Conversion Tool
Enables you to convert native SOLiD™ data into a community-driven standard (Short Read Format) for NCBI submission. Available as source code.

SOLiD™ BaseQV Tool
Tool for the conversion of SOLiD™ output files to base sequences data with associated quality values.

Genome Browsers

SOLiD™ Alignment Browser
A genome annotation viewer and editor which is based on the Apollo Genome Annotation Curation Tool.

UCSC Genome Broswer
The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide.

Mapping Tools

Color Space Mapping Tool
Enables you to map SOLiD™ color space reads to whole human genomes. Available as source code.

SHRiMP
The SHort Read Mapping Package.

BFAST
Enables you to map short reads to reference sequences quickly and accurately.

SOCS
This software uses iterative mismatch tolerances to speed up high tolerance mapping. It finds optimal alignments for each read across one or more reference files. It also provides maps of sequence census and isolated mismatches.

NOTICE TO USER | TERMS AND CONDITIONS | DISCLAIMERS

The Applied Biosystems resources provided here are all unsupported software development tools. They are not validated products and are provided "as is" and without warranty. Without limiting the foregoing, your use of such resources is subject to any applicable license or terms of use.

Links to third-party Web sites and any resources or products that they may provide are intended for convenience only and do not imply endorsement or approval by Applied Biosystems and we neither support nor make any warranty for such resources. Applied Biosystems is not responsible for their contents. All queries and end-user support requests regarding third-party resources and products should be addressed to the relevant third party. Applied Biosystems is not responsible for providing any end-user support.

The use of all the resources provided herein and any associated materials is at user's own risk, without recourse to Applied Biosystems. Your use of any resources provided herein, including the software tools, is conditioned on your acceptance of the above terms, including the applicable license terms, if any, and your use of any of the resources herein indicate your understanding and acceptance of these terms.

1000 Genomes Project

1000 Genomes Project Data
This 1000 Genomes Project data contains the first set of SNP calls for 4 individuals that are part of the high coverage pilot project. These SNPs represent the preliminary analysis of a portion of the data so far collected and are released in accordance with the Ft. Lauderdale agreement for community resource projects. The data consist of README files, fastq files (nucleotides and qualities) suitable for use with most aligners, and md5 checksum data.

Resequencing

SOLiD™ Human Sample NA18507
Human sample NA18507 was sequenced using the SOLiD™ System. Data sets are available to the scientific community through the public database hosted by the National Center for Biotechnology Information (NCBI). The public availability of this sequence data will help scientists gain a greater understanding of human genetic variation and potentially help explain differences in individual susceptibility and response to treatment for disease. The data may also be used to further enable the development of analytical tools for next generation sequence data.

E.Coli DH10B Mate Pair Data
Sample resequencing data from E.Coli DH10B. It is the statistical analysis output from a quarter of a slide of a 50 bp mate-pair run.

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

Small RNA Analysis

Human Small RNA Data Set
Total RNA was isolated from human tissue samples and subsequently fractionated using flashPAGE. The small RNA fraction was converted to double stranded DNA templates suitable for sequencing using the Applied Biosystems SOLiD™ Small RNA Expression Kit. Subsequently small RNA libraries were clonally amplified by ePCR and run on a SOLiD™ instrument. Each library generated between 40 and 45 million of 35 bp (colors) length reads for a total of 175 million reads.

Whole Transcriptome Analysis

Whole Transcriptome Data Set
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)


Company/Software		Supported Applications
	BioTeam BioTeam provides services for integrating sequencers, computing and storage systems, and managing data with WikiLIMS™	Data Management
	BioTique Systems BioTique has a commercially developed software, HT-BLIS (High-Throughput HT-BLIS), which enables academic and research organizations to process the massive amounts of data being generated by high-throughput genomic analysis systems	Data Management
	CLC bio Comprehensive Next Generation Sequencing analysis solutions with native Color Space analysis of SOLiD™ System data. CLC bio's customizable solutions include accelerated analysis of Genomics, Transcriptomics, and Epigenomics data. CLC bio offers everything from user-friendly desktop applications to full High-Performance Computing enterprise solutions, completely integrated with existing workflows.	ChIP-Seq De Novo Assembly Whole Transcriptome Analysis
	GenoLogics Lab and data management solutions for life sciences research. The Genologics platform automates workflows and data capture by integrating to technology platforms such as the SOLiD™ System.	Data Management
	Genomatix We offer high throughput sequencing service with the SOLiD™ System as an Applied Biosystems Service Provider in Europe. We have implemented and optimized all the applications for this platform, and we collaborate with two academic bioinformatics groups in order to provide the most complete information to our customers.	Small RNA Analysis Whole Transcriptome Analysis
	Genome Quest GenomeQuest is a web-based software application for managing and mining sequence data and a management system for sequence reference data.	Data Management
	Geospiza GeneSifter® Geospiza's GeneSifter software offers award winning ease-of-use, enabling you to understand the biological significance of your SOLiD™ System data and draw meaningful conclusions quickly.	Data Management Whole Transcriptome Analysis Small RNA Analysis ChIP-Seq
	InteRNA InteRNA provides a service-based bioinformatics solution, miR-Intess™, that converts large sets of raw sequencing data into interpretable formats, enabling researchers to integrate this information with existing proprietary and public data resources.	Small RNA Analysis
	Partek® Genomics Suite™ Partek® Genomics Suite™ takes your Next Generation Sequencing data all the way from aligned reads to gene ontology and pathway analysis and beyond. The RNA-seq, ChIP-seq and DNA-Seq user friendly data analysis workflows, will guide you through sophisticated statistical analysis into biological interpretation within our intuitive and interactive genome browser. In supporting all microarray and next generation sequencing technologies and assays, Functional Genomics turns concrete with our Integrative Genomics workflows.	DNA-Seq including SNP duo and trio calling RNA-Seq including Whole Transcriptome, Small RNA and Allele Specific Expression ChIP-Seq Methylation
	SoftGenetics SoftGenetics, world leader in Genetic Analysis Software features NextGENe 2nd Gen Analysis software for the SOLiD™ System. Software provides biologist-friendly interface; no scripting reduced bioinformatics costs; includes many unique technologies including its patent-pending Condensation Tool to increase analysis accuracy. Provides a host of applications: de novo, SNP & structural discovery, transcriptome, ChiP-Seq, mRNA and other applications.	ChIP-Seq De Novo Assembly Resequencing Whole Transcriptome