Avadis NGS

Category Cross-Omics>Next Generation Sequence Analysis/Tools, Cross-Omics>Workflow Knowledge Bases/Systems/Tools and Genomics>Gene Expression Analysis/Profiling/Tools

Abstract Avadis NGS is a desktop application for the analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms.

It supports workflows for RNA-Seq, DNA-Seq, and ChIP-Seq analysis and is designed with the biologist in mind.

Import Aligned Data -- Avadis NGS allows import of reads that have already been aligned to a reference genome. The file formats supported are SAM, BAM, and BED files, as well as outputs from Illumina’s ELAND pipeline.

Avadis NGS handles single-end, paired-end and mate-paired data from a variety of sequencing vendors including Illumina, Roche 454, ABI SOLiD, Ion Torrent, and Pacific Biosciences.

Once the aligned data is imported into Avadis NGS, the relevant downstream analyses can be performed using the workflows described below.

RNA-Seq Workflow -- Transcriptome data can be visualized and analyzed using the RNA-Seq workflow, in Avadis NGS. In addition to classical differential gene expression analysis, Avadis NGS can be used to find alternatively spliced genes (via Alternative Splicing Analysis - see below...), to discover novel genes and exons, and to identify novel splice junctions.

In many disorders like cancer, the genetic make-up of a cell is changed in such a profound way, that genes fuse together, resulting in a hybrid protein with potentially devastating effects on the cell -- these gene fusions can also be discovered by Avadis NGS.

DNA-Seq Workflow -- Avadis NGS supports the DNA-Seq workflow for detecting small variations including SNPs, multi-nucleotide polymorphisms (MNPs), and InDels [deletion/insertion polymorphisms (DIPs)] from whole genome and exome data.

These variants, of both homozygous and heterozygous kinds, can be annotated with information from dbSNP to identify known and novel variants (via the Variant Support View - see below...).

In addition, the effect of these variants on transcripts can be assessed, resulting in classifications such as a non-synonymous coding SNP or frameshift InDel.

Larger structural variations, including large insertions, deletions, inversions, and translocations, can be detected for experiments that use paired-end or mate-paired libraries.

ChIP-Seq Workflow -- The ChIP-Seq analysis workflow supports identification of transcription factor binding sites and histone modification, by using peak detection algorithms such as PICS and MACS.

For transcription factors, this can be followed up by looking for potential motifs in these peak regions, by using the GADEM motif-detection algorithm. The genes close to the detected peaks can be identified as good candidates for transcription factor regulation.

Avadis NGS Discovery -- Avadis NGS provides custom visualizations to verify analysis results from the above workflows, including a feature-rich embedded Genome Browser - (see below...).

Avadis NGS comes pre-packaged with annotations for several standard organisms and supports the ability to create annotations for other organisms.

Gene and transcript annotations from multiple sources like UCSC, Ensembl, and RefSeq are supported.

Genes identified by any of the workflow steps above can be subject to biological interpretation and discovery using steps such as Gene Ontology (GO) enrichment, GSEA, NLP derived interaction network analysis and significant Pathways Analysis - (see below...).

Avadis NGS Analysis Features include:

Genome Browser --

Genome Browser is a representation of a complete genome on which the sequenced reads can be visualized. Annotation data, such as cytobands, genes, and transcripts, can be superimposed, as well as results from various analyses, such as peak regions, SNPs, and gene fusions.

Semantic zooming - Genome Browser is equipped with semantic zooming, displaying visualizations based on the zoom level. At low zoom level, only the coverage line plot is shown. At intermediate zoom level, both the coverage and reads are shown, with colors indicating the mismatch bases. At high zoom level, all bases are displayed as colored letters.

Intermediate zoom level - Reads start to show up below the coverage plots. The reads are shown as colored bars. Gray indicates the reads match the reference sequence perfectly. Colors within the reads highlight mismatched bases.

Visualizing spliced reads - If reads are spliced (typically in RNA-Seq experiments), the read is shown split between the two (or more) positions, separated by a grey line. For paired-end reads, the two reads are separated by a black line.

Paired read visualization - For paired-end or mate-paired data, the mate status is indicated with colors. Reads with missing mates are colored in red, while mates that align far from each other are colored black. Clusters of reads of the same color help users verify structural variations predicted by the tool.

Mismatch coverage - A stacked histogram on the coverage plot can show locations with a large number of mismatches. Colors of the histogram represent the proportion of bases. The presence of the histogram indicates possible SNP locations.

Variant Support View -- The Variant Support View lists the SNPs and small InDels that were detected during SNP analysis. The bottom panel (Not shown here...) summarizes all the reads that span the selected variant location.

Reads with identical sequences in the neighborhood of the selected SNP are clustered into a single row with the cluster size shown to the right.

The view with its sortable columns and cluster sizes is especially helpful in verifying heterozygous SNPs and SNPs that fall in high coverage regions. Large clusters with multiple variant positions can be used to detect haplotype blocks.

Pathway Analysis -- Avadis NGS provides the capability to learn how genes interact with each other using information extracted from the literature as well as from canonical pathways.

Avadis NGS allows the user to ask and answer questions like: Which small molecules or other genes might interact with my list of genes? Interactions between genes and small molecules may provide insight into the functionality of the genes.

Extracting interaction data from literature - Strand has developed a natural language processing (NLP) technology that understands the grammar of English sentences and can extract this interaction information from literature (in the life sciences).

This information can be stored in a database and later used to infer relationships between genes, protein, small molecules, and processes.

The NLP tools are also made available so that users may add their own interactions to the database by parsing input text of their choosing (full-length articles, PDF files, HTML documents, Word documents, and text files).

Download pathway interaction data - Strand has used this NLP technology to construct an Interaction Database for a wide variety of organisms. This database is freely available for Avadis NGS users and can be downloaded from the Strand Server.

Information can be overlaid on the networks (as stated above...) and interaction networks can be saved for future reuse and become pathways that can be used in future analysis to determine if a list of genes contains a statistical significant over-representation of genes belonging to the pre-existing, newly created pathway.

Alternative Splicing Analysis -- Gene Behavior in a Structural Context - In RNA-Seq experiments, the differential expression of genes and transcripts can be shown in a special visualization plot. The transcripts are displayed in an “idealized” fashion, where the introns are reduced and only the exons are shown in their original sizes.

This allows for the display of the coverage of the reads on exons regardless of the size of the genes on the genome.

Gene and Transcript Expression - Expression values for a gene across conditions can be contrasted with the expression levels of individual transcripts above. Expression levels of individual transcripts are obtained via a deconvolution procedure.

Exon Expression - The expression levels for each exon for each of the conditions can be shown, making it easy to identify which exons are differentially spliced across conditions.

SNP Detection -- The SNP detection feature in Avadis NGS identifies the variants (SNPs/MNPs/InDels) in a sample by comparing the aligned reads against the reference genome.

Based on the distribution of As, Ts, Gs, and Cs at a particular position, and the likelihood of a sequencing error, a judgement is made with regards to the existence of a SNP.

The SNP detection algorithm in Avadis NGS works on a per-sample basis. For each sample, data for each chromosome is analyzed, with a capability for parallel computation per chromosome. The computation is optimized for memory usage by segregating the data into windows based on maximum read size.

BIOBASE Genome Trax TM and Avadis® NGS --

Strand Scientific Intelligence, Inc. and BIOBASE GmbH have joined forces to bring you one of BIOBASE’s latest biological databases - BIOBASE Genome Trax - as integrated annotations, accessible in just one click from within the RNA-Seq, DNA-Seq, and ChIP-Seq workflows in Avadis NGS.

Avadis NGS gives you the tools for identifying genomic variants like SNPs, MNPs, InDels, and larger structural variations in your NGS data.

Annotating these variants with the human curated annotations of Genome Trax will give you immediate insight into which of these variants is already known to be involved in a disease-related pathway or located in or near a known regulatory site.

The manufacturers have integrated the following five (5) annotation tracks for human data (builds hg18 and hg19) into Avadis NGS:

1) 3,000+ regulatory sites from TRANSFAC®;

2) 80,000+ disease linked mutations from HGMD® Professional;

3) 600,000+ ChIP-Seq fragments with best binding site predictions;

4) Post Translational Modifications (PTMs); and

5) Transcription Start Sites (TSSs).

They can be downloaded from the Strand Server. After that, any region list can be annotated with one or several of the Genome Trax annotations.

Genome Trax annotations are updated quarterly by the BIOBASE experts and the manufacturers implement these updates in line with their schedule.

System Requirements

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Manufacturer Web Site Avadis NGS

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G6G Abstract Number 20784

G6G Manufacturer Number 104295