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Avadis NGS December 27, 2011
December Newsletter

We wish you a happy new year!

We are very excited for 2012 because we think it will be the year that Avadis NGS makes a permanent dent in the universe of sequencing. At the top of our list of new year's resolutions is sustaining the high level of satisfication our customers have experienced with high quality technical support and continuous improvements to the Avadis NGS software product. Please keep us accountable to our resolutions!

New Video Tutorials

Alignment of Raw Sequence Reads using COBWeb
Watch this video to learn about COBWeb and its comparison to several existing open source tools for alignment. We will also walk you through the steps for performing alignment within Avadis NGS 1.3 and for quality inspection and downstream analysis with the alignment results.

Small RNA-Seq Data Analysis
Watch this video to learn about our new aligner and analysis features specifically for small RNA reads. The ability to run COBWeb alignment on small RNA data, quantify known small RNA, identify novel small RNA, identify target genes, and other analysis features, are part of the recently released Avadis NGS 1.3 Beta.

Recent Blog Posts

How Identical are Identical Twins? by Ramesh H.
"We're looking at exome sequencing data generated by our collaborators at Uppsala University in Sweden. Monozygotic twins were earlier thought to be genetically identical; now we know that isn't completely true. How does one identify small mutations that are present in one of the twins but not in the other..." Read more

A Case for Long CIGARs: Achieving 50% Compression of BAM Files by Vamsi V.
"How much disk space is really needed to store the entire information of the 1.23 million matches present in a 151 Mb file? If I can get to 50% of the BAM file size painlessly, I'll be a happy man. BAM internally uses a gzip like compression, but the format is optimized for indexed retrievals..." Read more

1.3 Beta Released!

The Avadis NGS version 1.3 Beta is now available for download. This update includes several new workflow steps and visualizations that will enable you to go from alignment to analysis of data from newer sequencing experiment types, all within the same desktop software program.

  • Experiment-specific analysis pipeline for small RNA data that now allows you to run QC steps, perform expression analysis and detect novel small RNA regions
  • COBWeb – a built-in sequence data alignment algorithm based on the Burrows-Wheeler Transform (BWT) designed for gapped alignment of DNA and small RNA reads in FASTA and FASTQ files
  • Three new RNA-Seq quantification and normalization options – DESeq, Quantile, and TMM
  • Significantly faster to import data – including genomic annotations and sample data in BAM, SAM, and ELAND files
  • Workflow steps for differential SNP analysis to handle a variety of use cases – including normal-tumor and multi-group comparisons – with improved precision
  • Capability to import annotations from GenBank files and analyze organisms like bacterial genomes
  • Import of raw data from benchtop sequencers MiSeq and Ion Torrent
If you are interested in either trying the Beta version of 1.3 with your own data or scheduling a demo presentation for your organization, send us an email that describes your experiments and desired research endpoints.

If you are interested in buying Avadis NGS for your lab, please contact sales for plans and pricing.

Happy holidays!
- The Avadis NGS Team

© 2011 Strand Scientific Intelligence, Inc.

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