A list of the RNA-Seq data analysis software packages available from commercial providers. Again, if I’ve missed something, please send me a note and I will be happy to add to this list.
Avidis NGS – http://www.avadis-ngs.com/applications/rna_seq – Find fused genes via spliced and paired reads spanning the fused genes. Analyze coverage patterns to detect novel genes and exons not present in NCBI, UCSC, and Ensembl annotations. Seamlessly create and manipulate genomic region lists. Filter region lists based on different attributes. Determine gene and deconvoluted transcript expression profiles; identify alternative splicing patterns. Identify differential gene profiles via statitistical tests, cluster genes with similar profiles. Carry out GO analysis to identify significant GO terms.
CLC Genomics Workbench – http://www.clcbio.com/index.php?id=1240 – Our RNA-seq analysis now supports the use of paired-end data for RNA-seq. A combination of single reads and paired reads can also be used, and expression values can now be stratified into transcript level expression values, both for single and paired reads, allowing users to compare two different samples across transcripts. Another important new feature is our batching functionality of all our high-throughput sequencing tools, enabling researchers to perform the same analysis on several elements in one batch, which is an easy way to analyze multiple datasets in one go and thereby save time for setting up and running the same type of analysis multiple times.
DNAnexus - https://dnanexus.com/features/researcher/analyses – tag-based applications. RNA-seq is now a cost-effective way to measure gene expression, discover alternative splicing, and identify previously unassayed transcriptional activity. ChIP-seq provides a general way to study interactions between DNA and other molecules. With DNAnexus, these and other tag-based applications can be analyzed through our cloud-based infrastructure with the click of a button. Visualize the results in the DNAnexus browser, or export the results in tabular format and integrate your data across multiple experiment types, for example combining RNA-seq expression data with ChIP-seq binding affinity on the same genes.
DNASTAR QSeq – http://www.dnastar.com/t-products-qseq.aspx – QSeq is DNASTAR’s Next-Gen application for RNA-Seq, ChIP-Seq, and miRNA alignment and analysis. QSeq is fully integrated with ArrayStar, enabling you to take advantage of its powerful visualization and analytical tools, including using Gene Ontology (GO) annotations for ontology comparisons and gene characterization. Using QSeq, researchers can select gene sets and export associated reads through the rest of the DNASTAR software pipeline for sequence assembly, alignment, and detailed analysis.
GeneSifter – http://www.geospiza.com/Products/default.shtml – Analysis Kits offer a solution for scientists faced with large volumes of unprocessed data from AB SOLiD or Illumina Genome Analyzer DNA sequencing. Through Geospiza’s rapid analysis service, you can complete Next Generation Data Analysis as a service per file or per run. GeneSifter Analysis Edition now supports Whole Transcriptome Analysis with a more detailed view of each gene, including predicted splicing events and exon usage – increasing your access to the depth of next generation sequencing. This new analysis capability also includes an integrated gene viewer – to see your data as it relates to the genome and then tie it to publicly available information.
Geomatix Genome Analyzer – http://www.genomatix.de/en/produkte/genomatix-genome-analyzer.html – The Genomatix Genome Analyzer is our integrated solution for comprehensive second-level analysis of Next Generation Sequencing (NGS) data from ChIP-Seq, RNA-Seq or genotyping experiments. Each analyzer is brimming with state-of-the-art technology that sheds light on biological context – essential to help you understand the big picture.
GenomeQuest RNA Seq – http://www.genomequest.com/science/workflows/rna-seq/ – RNA-Seq stands to replace existing transcript profiling technologies as it measures all RNA in a sample, not just the RNA that can be probed for using traditional chips. GenomeQuest provides a powerful workflow that integrates best-of-breed open source technologies in a commercially supported environment to measure gene expression and to discover novel splice variants.
Ingenuity IPA 9.0 – http://www.ingenuity.com/products/pathways_analysis.html – IPA will support RNA-Seq processed datasets containing Ensembl, RefSeq or UCSC IDs. Researchers will now be able to analyze and interpret their RNA-Seq data. IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity® Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research.
Partek Genomics Suite (Partek GS) – http://www.partek.com/ngs#rnaseq Using a whole-transcriptome sequencing approach, sequence data are analyzed for differential expression and alternative splicing based on known mRNA annotation. Sequencing reads that are not mapped to any known mRNA annotation are used to uncover the novel transcriptional regions. Partek GS will identify and quantify sequence variants (coding SNPs) within RNA-seq samples. With a collection of SNPs identified, Partek GS will then find allele specific expression that drive phenotypic change within the transcriptome. Both paired end and junction reads are supported.
RNA Baser Sequence Assembler – http://www.rnabaser.com/ – RNA Baser Sequence Assembler represents an extension of DNA Baser Sequence Assembler, specialized in processing rRNA sequences. It is optimized for early integration of contextual metadata. This way, the metadata will stay attached to the primary sequence information throughout the complete workflow of sequence analysis, until final submission. In addition, RNA Baser Sequence Assembler is optimized for data exchange with standard non-commercial software used for rRNA sequence analysis and submission.
SeqSolve – http://www.integromics.com/ngs – for Next Generation Sequencing: a unique approach for the downstream analysis of RNA-seq data. – characterization of the reads, distributions into annotated genic regions, coverage profile within genes, read density over genomic sites, statistical support for differential gene expression, antisense transcription analysis, quality controls of the samples with library complexity, strand specificity, coverage asymmetry… and much more! Get the best from your RNA-seq data with SeqSolve.
Softgenetics NextGENe – http://www.softgenetics.com/NextGENe_11.html – NextGENe Software includes analysis tools designed for RNA-Seq analysis of data DNA sequencing data from Roche/454 GS FLX, FLX Titanium & Junior, Applied Biosystems’ SOLiD System and Illumina GA & Hi-Seq systems. Transcriptome sequencing data is aligned to the reference sequence to allow for detection of alternative splice sites, gene fusions, exon skipping and intron retention. NextGENe detects which exons are present in the sample data and chooses the appropriate reference transcripts. Accurate expression levels can be evaluated and mutations are reported. Alignment of RNA-Seq data with NextGENe uses a specialized algorithm to accurately align reads along exon boundaries.