Strand Scientific Intelligence is happy to announce the release of Avadis NGS. NGS analysis for the rest of us!
Avadis NGS is an application for the analysis of NGS data for RNA-SEQ, ChIP-SEQ and DNA Variant analysis and is specifically designed for and by Life Science researchers and developed by Strand Scientific Intelligence.
We have developed the Avadis NGS product on the same platform as we used for the development of GeneSpring GX. Many of you may know GeneSpring GX as the popular analysis package for Array based gene expression analysis from our partner Agilent Technologies, who sells and markets the application we develop for them. Since Avadis NGS is built on the same platform as GeneSpring GX, people who know how to use GeneSpring, can immediately get started with Avadis NGS, since it has the same look and feel as GeneSpring and many of the features behave in the same way.
Avadis NGS allows you to analyze Next-Gen Sequencing data using pre-aligned data. We have chosen to support the SAM/BAM format as the main import format for pre-aligned data, since it has rapidly become the de-facto standard as the file format of choice for aligned data. Made popular by the 1000 Genome project, it is now being adopted by most, if not all, NGS vendors as the standard exchange format for their aligned data.
Avadis NGS supports three major NGS workflows;
The major objective in ChIP-SEQ experiments is to find regions on the genome that bind a particular protein or complex, such as Transcription Factors, RNA Polymerase subunits or Histones. The CHIP-SEQ experiment workflow in Avadis NGS, allows you to find those regions in the genome that have an overabundance of sequence reads aligned to it, by looking for peaks in the coverage, using a variety of peak finding algorithms, such as PICS and MACS. For transcription factors, this can be followed up by looking for a potential binding motif in and around those peaks, by using motif-detection algorithms, such as GADEM. In addition, the genes that are close to the detected peaks are good candidates for being regulated by those transcription factors and can be detected. The gene ontology and pathway analysis tools can then be applied to learn more about the set of regulated genes and their respective targets.
For the study of the Transcriptome, Avadis NGS supports the RNA-SEQ experiment type or Workflow. In addition to the almost “classical” differential gene expression analysis using the normalized expression levels, Avadis NGS allows for the detection of alternatively spliced transcripts as well. Both known and novel splice variants can de discovered and we also have functionality to discover complete new genes and transcripts.
In many disorders, such as cancer, the genetic make up of a cell is changed in such a profound way, that two genes are fused together, resulting in a hybrid protein with potentially devastating effect on the cell and these gene fusion products can be detected with Avadis NGS.
The third and last supported workflow is the detection of SNPs and small Insertion and Deletions or InDels. SNPs and InDels are discovered and annotated with information from the dbSNP or equivalent databases. In addition to the dbSNP annotation, the effect of a SNP or InDel on the coding regions can be assessed as well, resulting in such classifications as “NON-SYNONYMOUS-CODING SNP”, “FRAMESHIFT InDel” etc. Larger structural variations, such as large insertions and deletion as well as translocations and other re-arrangements can be detected for those experiments that use the paired end or mate-paired libraries.
For more information on Avadis NGS and a free evaluation copy, visit our website at http://avadis-ngs.com.
Avadis NGS is an application for the analysis of NGS data for RNA-SEQ, ChIP-SEQ and DNA Variant analysis and is specifically designed for and by Life Science researchers and developed by Strand Scientific Intelligence.
We have developed the Avadis NGS product on the same platform as we used for the development of GeneSpring GX. Many of you may know GeneSpring GX as the popular analysis package for Array based gene expression analysis from our partner Agilent Technologies, who sells and markets the application we develop for them. Since Avadis NGS is built on the same platform as GeneSpring GX, people who know how to use GeneSpring, can immediately get started with Avadis NGS, since it has the same look and feel as GeneSpring and many of the features behave in the same way.
Avadis NGS allows you to analyze Next-Gen Sequencing data using pre-aligned data. We have chosen to support the SAM/BAM format as the main import format for pre-aligned data, since it has rapidly become the de-facto standard as the file format of choice for aligned data. Made popular by the 1000 Genome project, it is now being adopted by most, if not all, NGS vendors as the standard exchange format for their aligned data.
Avadis NGS supports three major NGS workflows;
- ChIP-SEQ
- RNA-SEQ
- DNA-SEQ
The major objective in ChIP-SEQ experiments is to find regions on the genome that bind a particular protein or complex, such as Transcription Factors, RNA Polymerase subunits or Histones. The CHIP-SEQ experiment workflow in Avadis NGS, allows you to find those regions in the genome that have an overabundance of sequence reads aligned to it, by looking for peaks in the coverage, using a variety of peak finding algorithms, such as PICS and MACS. For transcription factors, this can be followed up by looking for a potential binding motif in and around those peaks, by using motif-detection algorithms, such as GADEM. In addition, the genes that are close to the detected peaks are good candidates for being regulated by those transcription factors and can be detected. The gene ontology and pathway analysis tools can then be applied to learn more about the set of regulated genes and their respective targets.
For the study of the Transcriptome, Avadis NGS supports the RNA-SEQ experiment type or Workflow. In addition to the almost “classical” differential gene expression analysis using the normalized expression levels, Avadis NGS allows for the detection of alternatively spliced transcripts as well. Both known and novel splice variants can de discovered and we also have functionality to discover complete new genes and transcripts.
In many disorders, such as cancer, the genetic make up of a cell is changed in such a profound way, that two genes are fused together, resulting in a hybrid protein with potentially devastating effect on the cell and these gene fusion products can be detected with Avadis NGS.
The third and last supported workflow is the detection of SNPs and small Insertion and Deletions or InDels. SNPs and InDels are discovered and annotated with information from the dbSNP or equivalent databases. In addition to the dbSNP annotation, the effect of a SNP or InDel on the coding regions can be assessed as well, resulting in such classifications as “NON-SYNONYMOUS-CODING SNP”, “FRAMESHIFT InDel” etc. Larger structural variations, such as large insertions and deletion as well as translocations and other re-arrangements can be detected for those experiments that use the paired end or mate-paired libraries.
For more information on Avadis NGS and a free evaluation copy, visit our website at http://avadis-ngs.com.