Avadis® NGS is a desktop software platform for analysis, visualization, and management of data generated by Next-Generation Sequencing (NGS) platforms. It supports workflows for Alignment, DNA-Seq, RNA-Seq, Small RNA-Seq and ChIP-Seq analysis and is designed with the biologist in mind. Alignment
Avadis NGS supports an inbuilt alignment algorithm called COBWeb that supports the alignment of both short and long reads with an arbitrary number of gaps and mismatches. It also includes support for paired end reads and a variety of trimming options and screening databases. DNA-Seq
The DNA-Seq workflow in Avadis NGS supports the detection of SNPs and small Insertion and Deletions (InDels). SNPs and InDels are discovered and annotated with information from dbSNP or other sources such as BIOBASE GenomeTrax annotations. The effect of a SNP or InDel on the coding regions can be assessed to identify "NON-SYNONYMOUS-CODING SNP", "FRAMESHIFT InDel", etc. In multi-sample scenarios, one can determine significant SNPs such as High Confidence Common Variants, Low Frequency Common Mutations, etc. Larger structural variations including large insertions, deletions, translocations and inversions can be detected with paired end data. RNA-Seq
Avadis® NGS supports the RNA-Seq workflow for the study of the transcriptome. In addition to the classical differential gene expression analysis using the normalized expression levels, Avadis® NGS Software allows for the detection of alternatively spliced transcripts as well and provides a unique visualization of the spliced transcripts with the special gene view. Both known and novel splice variants can be discovered and there is functionality to discover complete new genes and transcripts as well as gene fusion products. Small RNA-Seq
The Small RNA-Seq workflow in Avadis® NGS supports quantification of small RNA data including miRNA, tRNA, snRNA and snoRNA. Novel small RNA genes can also be detected and analyzed. It supports the ability to perform differential gene expression analysis for both known and novel genes for different experimental setups. Additionally, for miRNA genes, a variety of target enrichment databases are supported. The identified targets can be further analyzed with the Gene Ontology and Pathway Analysis tools. ChIP-Seq
The ChIP-Seq experiment workflow in Avadis® NGS Software allows for the detection of peak regions in the genome using a variety of peak-finding algorithms such as PICS and MACS. For transcription factors the motif-detection algorithm GADEM can be used to identify potential motifs at these binding sites. The genes regulated by those transcription factors can be further analyzed using biological interpretation steps.
More details about Avadis® NGS can be found at http://www.avadis-ngs.com/