Avadis NGS
|
Application data |
|
| Created by | Yeshodari |
|---|---|
| Biological application domain(s) | ChIP-seq, Sequencing, DNA-Seq, Small RNA-Seq, RNA-Seq, RNA, Methyl-Seq, MeDIP-Seq, Pathway or network analysis |
| Principal bioinformatics method(s) | Sequence alignment, Sequencing quality control, Sequence analysis, Visualisation, Analysis, Biological interpretation |
| Technology | Illumina, 454, ABI SOLiD, Ion Torrent, PacBio, Ion proton |
| Created at | Strand Genomics, Strand Life Sciences |
| Maintained? | Yes |
| Input format(s) | SAM, BAM, Unaligned BAM, FASTA, FASTQ, BED, ELAND |
| Output format(s) | .txt, Tab separated, Tab-delimited, TSV, VCF, HTML |
| Software features | Rich Visualisation, Identify effects of SNPs on transcripts, Identify Structural Variants from Paired Reads (Insertions, Deletions, Translocations, Inversions), Identify binding site peaks in ChIP-seq data, Identify motifs around binding sites, Determine gene expression levels and identify differentially expressed genes De-convolve transcript expression levels and identify differential splice variants, Identify Novel Exons, Identify Novel Splice Junctions, Identify Fusion Genes Perform QC on Reads, determine on-and off-target reads, and filter anomalous reads, Determine Enriched GO Terms, Determine Significant Pathways |
| Programming language(s) | Java, R, Python |
| Licence | Commercial |
| Operating system(s) | Windows, Linux, Mac OS X |
| Contact: | sales@strandngs.com |
Summary: Strand NGS formerly Avadis NGS is a desktop software platform for alignment, analysis, visualization, and management of data generated by next-generation sequencing (NGS) platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-seq, and Methyl-Seq data analysis. Strand NGS is designed with the biologist in mind. 200px|right
"Error: no local variable "counter" was set." is not a number.
Description
Strand NGS formerly Avadis® NGS is an integrated Next generation sequencing analysis platform for data mining and visualization at the core of all bioinformatics products developed by Strand. The platform has been integrated with state-of-the-art algorithms for alignment, quality control, analysis and management of next-generation sequencing data on a wide range of computing infrastructures. Strand NGS supports import of raw read sequences from sequencing platforms like Illumina, Ion Torrent, PacBio, ABI, and 454 Life Sciences and supports fragment, single-end, paired-end, mate-paired, directional single/ paired end library types. Raw reads in formats FASTA, FASTQ, SAM, BAM, Unaligned BAM, BED, Counts data, VCF, VAL, or Eland formats can be imported into the tool. In addition, perform split read alignment for detecting long InDels and translocations.
Strand NGS also allows users to perform quality control on the imported data and filter reads before the main analysis is performed. Version 2.6 of the tool supports six experiment types: ChIP-Seq, RNA-Seq, small RNA, Methyl-Seq, MeDIP-Seq and DNA-Seq. Gene, transcript, SNP, homology, gene ontology (GO), and other annotations needed for analysis can be downloaded directly from within Strand NGS website.
The ChIP-Seq analysis workflow allows users to identify enriched regions using three different peak finding algorithms - a simple sliding window based approach, MACS, and PICS. Depending on the experiment design, these regions could be transcription factor binding sites, methylation sites, etc. Motifs present in the identified binding sites can be discovered using a parallel implementation of the GADEM algorithm. Entity lists containing the genes in the neighborhood of the binding regions can be created and used in downstream gene ontology, GSEA, pathway analysis.
The RNA-Seq experiment workflow allows users to measure expression levels of known genes and transcripts. It also allows discovery of novel exons, genes and splice junction. The Genome Browser in Strand NGS enables users to validate the predictions by allowing viewing of the results in the context of annotations from multiple sources such as NCBI, the UCSC Genome Browser, and Ensembl. Statistical tests, specifically designed to handling count based data, can be used for differential gene expression and alternative splicing analysis. A special "Gene View" visualization presents consolidated information about a gene and helps in the verifications of predictions.
The DNA-Seq experiment workflow has links for SNP and structural variation detection algorithms. The SNP prediction step finds homozygous and heterozygous SNPs and identifies overlaps with the provided dbSNP annotations. SNPs falling in genic regions are further analyzed and their effect on transcripts is described (similar to the Ensembl SNP Effect Prediction web-service). The structural variation analysis algorithms identify homozygous and heterozygous InDels, inversions and translocation events. In addition, Copy Number Variations can be detected using tumor-normal pairs.
Visualization tools, namely Genome Browser, Gene View, and Variant Support View, are a key aspect of the software. Other visualizations available with tool are scatter plot, MvA plot, profile plot, histogram, heat map, box and whisker plot, and Venn diagram. Aided with visualizations, users a pictorial feel for statistical trends in the data.
Genome Browser in Strand NGS is an interface to visualize data, results, and annotations associated with the genome in one place. Annotation data, such as cytobands, genes, transcripts, etc., as well as results from the analyses, such as Peak regions, SNPs, Gene Fusions, etc. can be superimposed. Users can drag and drop data into the browser and also perform search operations. To navigate in the Genome Browser, users can scroll, pan, and zoom. Users may also color, filter, and label data points of interest. Gene View is used to visualize individual genes and their transcripts. Users can see read coverage for known, as well as novel, exon partitions.
Strand NGS also provides access to organism-specific interaction databases containing relations between proteins, small molecules, enzymes, complexes, biological processes, molecular functions, and gene families. The two million interactions present in these databases can also be augmented by importing pathways in GPML format (WikiPathways), XML format (BioCyc), BioPAX format from Reactome, Cancer Cell Map, etc. Gene lists generated by analysis steps can be used as the starting point for many pathway analysis operations.
Links
References
none specified
To add a reference for Avadis NGS, enter the PubMed ID in the field below and click 'Add'.
Search for "Avadis NGS" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
