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Avadis NGS October 5, 2012

New Release

The next version of Avadis NGS, v1.4.5, is due to release next week. This version includes several small patches for v1.4 of the product and some exciting new features. The key new features are highlighted below.

Functional Predictions for SNPs

You can now filter your SNP results to find damaging variants based on the functional predictions from the popular prediction algorithms like SIFT, Polyphen2, LRT, and MutationTaster. Avadis NGS uses dbNSFP for this purpose, which is an integrated database of functional annotations from multiple sources for the comprehensive collection of human non-synonymous SNPs (developed by Liu et. al.). This feature is available as the workflow step 'Find Damaging Variants' in experiments with hg19 build.

Above: Identify deleterious non-synonymous SNPs.

Support for Illumina directional protocols

New library layout options for directional paired end protocols have been introduced for Illumina samples. Alignment, quantification, and gene fusion detection have been appropriately enhanced to take the strand-specific nature of the data into account.


Import of sorted BAM files has been speeded up significantly. RNA-Seq alignment has been speeded up, with additional optimizations for the directional library layouts where the orientation of the read is known.

Existing users of Avadis NGS v1.3.1 and v1.4 will be automatically prompted for the update when the release goes live next week.

Illumina-Seek the Future: MiSeq Grant Program

Illumina has announced a MiSeq Grant Program that provides the opportunity for 3 researchers to win a MiSeq system package. Strand is happy to be associated with this program and will offer each of the winning entries a fully functional license for Avadis NGS in collaboration with Illumina.

To participate in the program:

  • Visit the MiSeq Grant Program webpage to access the official entry form.
  • Submit a 500 word write-up on how you would use a MiSeq system to discover, innovate, and accelerate your research.
  • Winners will be announced at the American Society of Human Genetics annual meeting, November 6-10, 2012 in San Francisco, California, USA.
All submissions must be sent to Illumina by 11:59 pm PT on October 15, 2012.

Meet Us at Illumina UGMs

This October, we will be at Illumina User Group meetings, held at New York and Boston on October 9th and 11th respectively, to connect with NGS scientific community to share exciting news about our future updates and find out more about what you can expect from our NGS analysis tools.

If you plan to be there and would like a dedicated time allotted to you to address your NGS analysis related questions, please let us know. We will arrange a time to connect with you.

- The Avadis NGS Team

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