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Avadis NGS February 8, 2011
Strand Scientific Intelligence presents the latest way to keep up with the world of next-generation sequencing (NGS) data analysis using Avadis NGS! Our regular newsletter will keep you informed about updates to the Avadis NGS software as well as upcoming events and features on our product roadmap.

About Avadis NGS

Avadis NGS is the software package brought to you by the same team behind the development and support of Agilent's GeneSpring software suite. We have designed Avadis NGS to empower biologists, who are intrigued by the possibilities of next-generation sequencing, to discover and interpret information from sequence data.

News & Updates

Yeast strain in the collection of reference genomes included with Avadis NGS installation
We recently added the reference genome and annotations for the Saccharomyces cerevisiae S288ca strain of yeast. These annotations and updates to human, mouse, rat, drosophila and zebrafish, can be downloaded using the Annotations Manager in Avadis NGS.

Support for other organisms
What about other organisms? If your organism of interest is not covered in the Annotations Manager there are two options for you. There are tools to build your annotations in Avadis NGS, or you may ask us to assemble the required information. Contact us to learn more and submit your request. In general, gene and transcript annotations are required for creating a new experiment; for SNP calling, chromosomal sequences are required as well (all in the form of FASTA files).

Avadis NGS version 1.1.1 released
The version 1.1.1 update includes some important changes to the Quantification and Fold Change Analysis features of the RNA-Seq workflow. As a result, the Quantification feature can now also be applied to intron-less genomes, such as bacterial genomes, and users are now able to increase the cut-off for the minimum number of pairs above the default value of 1 in a Fold Change Analysis.

Those currently working with version 1.1.0 will be prompted to update the next time the application is started. If you are still working with version 1.0.0, you will need to download the version 1.1.1 installer from the Downloads section of the website . For more information, refer to the user guide on our website or contact our support team for help.

Feature Highlight

SNP detection and targeted re-sequencing with Avadis NGS and Agilent SureSelect
Using Avadis NGS, you can detect novel SNPs and variations in your sequence data, and then determine regions of interest in the genome to study more deeply. By performing targeted re-sequencing using Agilent's SureSelect target enrichment technology, you will be able to validate relevant variations in your sequence data, as well as avoid the cost of re-sequencing the whole genome. Extend the functionality of Avadis NGS to find exonic regions of interest by downloading the 'FindExonicRegions' script from the Avadis NGS scripts library.

Upcoming Events

Attend a free webinar in February!
Want to find out more? Attend one of our free interactive webinars hosted by the Avadis NGS product manager, Dr. Thon de Boer. The webinars last about 45 minutes and introduce you to the most important features of Avadis NGS, like the guided workflows for RNA-Seq, ChIP-Seq and DNA-Seq experiments, SNP detection, identifying novel genes and splice junctions, and analysis of pathway interactions. At the end of the presentation you will have the opportunity to ask Thon any questions related to NGS data analysis.

Date/Time Pacific Standard Time
(San Francisco, GMT-08:00)
Eastern Standard Time
(New York, GMT-05:00)
European Time
(Berlin, GMT+01:00)
9 Feb 2011
07:00 hrs 10:00 hrs 16:00 hrs
16 Feb 2011
08:00 hrs 11:00 hrs 17:00 hrs
23 Feb 2011
07:00 hrs 10:00 hrs 16:00 hrs

If you can't make it for one of these dates or you are in the Asia Pacific region, you have the option to request a private webinar session for you and your colleagues by selecting "I would prefer a private session for my organization" from the 'Preferred Date' drop-down menu on the registration page. Alternatively, you could
watch a recording of one of our previous webinars.

Coming soon

Print and video tutorials
To help you quickly get started with Avadis NGS on your own, we are creating a series of short videos and step-by-step tutorials that will explain the quality control and downstream analysis workflows for the three experiment types supported in Avadis NGS: ChIP-Seq, RNA-Seq and DNA-Seq.

Our first set of videos will showcase Avadis NGS' various data quality inspection and control features. By watching the demonstrations on how to use Avadis NGS to check your sequencing data for base quality, alignment status, alignment score, and fix mate status, you will learn how to make sure your final results are as accurate as possible. Keep an eye out for these videos on our website soon!

Just ask!

We want to hear from you! If you have any questions at all please do not hesitate to contact us. Or if you are already working with Avadis NGS, why not share how your work has benefited?

We look forward to hearing from you!

- The Avadis NGS Team

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