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Avadis NGS August 8, 2012

Release Announcement

We are pleased to announce the release of Avadis NGS v1.4. Ever since the release of the earlier 1.3 version we have been cracking away at several new features and enhancements that are documented in the release notes. Some of the key features have been highlighted below.

We would like to especially thank our partners, with whom we have worked in close association to bring the latest and the best in NGS data analysis tailored to each sequencing platform for our customers.

RNA-Seq Alignment

Avadis NGS now provides complete end-to-end analysis of RNA-Seq data all the way from the reads to biological interpretation. The built-in aligner, COBWeb, has been extended to support alignment of RNA reads. Reads obtained from single/paired-end libraries or directional RNA-Seq protocols can be imported into the new RNA Alignment experiment.

COBWeb not only allows alignment of RNA reads against a specific transcriptome, but also can detect novel exons, and alignments involving novel splice junctions.

Target Region Alignment

Reads from targeted resequencing applications can be aligned much faster now. DNA alignment comes with a new option to align the reads to a set of target regions as opposed to aligning against the whole genome.

The target regions can also be padded on both sides if required before doing the alignment.

Pipeline Execution

Avadis NGS now introduces a pipelining feature where multiple workflow steps can be combined into a pipeline and executed in the background. You can continue using the application while the pipeline executes in the background.

A comprehensive DNA-Seq analysis pipeline consisting of read filtering, SNP detection, and SV detection is provided. More pipelines involving compute-intensive workflow steps will be introduced in subsequent releases.

Support for Variant Panels

Comprehensive support for variant panels is now provided. Variant panels containing known variants related to particular diseases can be added as variant allele list (VAL) annotations. Information about regions which are being targeted for the study of these variants can be brought in as a Target Region annotation. These annotations can be used to first verify that there is sufficient coverage in all the targeted regions. Then the presence of the known variants in the sample under investigation can be determined.

Amino acid sequence

The transcript track in the Genome Browser has been enhanced to show amino acid sequences also. When zoomed in to the appropriate level, the coding portions of the transcript show the amino acid symbols for all the codons with the codon regions being colored as per the color map of Ensembl. Also, the exons are numbered within each of the transcripts.

These can be used to quickly visualize the effect of SNPs in the Genome Browser.

Enhanced Variant Support View

You can now evaluate the SNPs or other small variants in one more dimension by looking at the quality of the variant location in the context of its neighborhood. This can be done by annotating the variant support view with base quality or mapping quality, along with the strand information.

New QC plots

Two new QC plots have been added to get better insights into the quality of the reads and the alignment. Read length distribution shows a histogram of read counts for various read lengths. Insert length distribution shows a distribution of insert lengths in case of paired reads.

How to Update

For new users

Download the latest installer for your platform from here and follow the on-screen instructions.

For current users

If you have a version lower than v1.3.1, please upgrade to v1.3.1 first from within Avadis NGS before upgrading to v1.4. To upgrade from v1.3.1 to v1.4, follow the steps given below.

  • Download the product update file from here for your appropriate platform.
  • Launch Avadis NGS v1.3.1 and upgrade to v1.4 by using the Help Menu > Update Product > From file... and provide the downloaded update file.
Note that due to some technical reasons, the automatic prompt for product update will not be available till 31 Aug. Please contact support in case you need any help with the product update.

- The Avadis NGS Team

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