Avadis NGS supports an extensive workflow for the analysis and visualization of DNA-Seq data – such as from whole genome, whole exome or targeted resequencing experiments. The workflow includes the ability to detect variants (SNPs, MNPs and short InDels), annotate them with dbSNP, and identify the effect on transcripts such as non-synonymous coding SNPs. Further downstream analysis such as GO, pathway analysis, etc can be performed on the set of affected genes. Large structural variations, including large insertions, deletions, inversions, and translocations, can be also detected with paired-end or mate-paired data.
Evaluate efficacy of targeted re-sequencing, and identify regions with low coverages across samples.
Identify homozygous and heterozygous SNPs, InDels and MNPs. Generate cumulative statistics, distributions, and rich plots.
Drag and drop SNP results into the genome browser. Visualize SNPs, MNPs, and InDels along with coverage, reads as well as other annotations.
Identify significant SNPs using an intuitive filtering framework that handles multiple use cases such as normal-tumor, multi-group comparisons, low-frequency mutations, rare variant analysis, and somatic mutations.
Variant Support View
View the delta-neighbourhood of SNPs in high coverage locations. Collapse reads into clusters to quickly verify predicted SNPs. Color with base quality or mapping quality, and annotate with strand information for more insight.
SNP Effect Analysis
Predict the effect of SNPs on the provided transcript annotations and identify SNPs of interest. Link out to dbSNP for more details.
Structural Variant Analysis
Detect structural variants in paired end data and identify large structural variants, including large deletions, insertions, inversions, and translocations.
Import VCF/VAL Files
Load VCF files and perform downstream analysis in an integrated manner; load VAL files and determine occurrence of variants of interest in the sample.
Manipulate Region Lists
Seamlessly create and manipulate genomic region lists. Filter region lists based on different attributes.
Configurable pipelines for compute-intensive tasks using the Pipeline Manager. Allows interaction with the user interface even as pipeline executes in the background.
Use the packaged database of 2 million interactions (with supporting PubMed references) to find relationships between genes.