a tour of various bioinformatics functions in Avadis NGS

Not affliated with Avadis but this might be useful for you 




We are hosting an online seminar series on the alignment and analysis of genomics data from “benchtop” sequencers, i.e. MiSeq and Ion Torrent. Our webinar panelists will give a tour of various bioinformatics functions in Avadis NGS that will enable researchers and clinicians to derive biological insights from their benchtop sequencing data.

Seminar #1: MiSeq Data Analysis

Avadis NGS 1.3 provides special support for analyzing data generated by MiSeq™ sequencers. In this webinar, we will describe how the data in a MiSeq generated “run folder” is automatically loaded into the Avadis NGS software during small RNA alignment and DNA variant analysis. This is especially helpful in processing the large number of files generated when the TruSeq™ Amplicon Kits are used. We will describe how to use the Quality Control steps in Avadis NGS to check if the amplicons have sufficient coverage in all the samples. Regions with unexpected coverages can easily be identified using the new region list clustering feature. Webinar attendees will learn how to use the “Find Significant SNPs” feature to quickly identify high-confidence SNPs present in a majority of the samples, rare variants, etc.


Seminar #2: Ion Torrent Data Analysis

Avadis NGS 1.3 includes a new aligner – COBWeb – that is fully capable of aligning the long, variable-length reads generated by Ion Torrent sequencers. In this webinar, we will show the pre-alignment QC plots and illustrate how they can be used to set appropriate alignment parameters for aligning Ion Torrent reads. For users who choose to import the BAM format files generated by the Ion Torrent Server, we will describe the steps needed for importing amplicon sequencing data into Avadis NGS. Users of the Ion AmpliSeq™ Cancer Panel will learn how to easily import the targeted mutation list and verify the genotype call at the mutation sites. We will also show the new “Find Significant SNPs” feature which helps quickly identify high-confidence SNPs present in a majority of the samples, rare variants, etc.


Free registration - http://www.avadis-ngs.com/webinar

Webinar Introduction to Ion Torrent Informatics

Webinar by Life Technologies
Introduction to Ion Torrent Informatics
4 May 2011
Register via this web link

Event Title

Introduction to Ion Torrent Informatics

Event Description

The Ion Torrent semiconductor sequencing platform includes a preconfigured Torrent Server that processes data from the Ion PGM™ Sequencer. With each semiconductor sequencing run, data analysis occurs on the Torrent Server. Scientists can interact with Torrent Server through the remotely accessible Torrent Browser web interface. Both processing status and run performance are easily viewable through these web pages. From Torrent Browser, detailed analysis reports can be viewed or sequencing data can be downloaded to your local computer for downstream analysis. The Torrent Suite Software formats base call and alignment data using industry standard data formats giving users the flexibility to use a wide variety of analysis tools. For scientists who are looking for analysis solutions, several downstream software packages are available and will be briefly demonstrated to show how DNA variations can be identified.

Solutions for Applying Automation to Next-Generation Sequencing Sample Prep

FYI might be useful for some.
disclaimer: I am not affliated with the companies involved.
http://www.genengnews.com/ngs


Solutions for Applying Automation to Next-Generation Sequencing Sample Prep

In recent years, next-generation sequencing (NGS) technologies have rapidly evolved to provide faster, better, cheaper and more reliable mapping of DNA and RNA sequences thus enabling a diverse set of genomic discoveries. This has been largely driven by innovations and improvisations at the technical end. However, challenges still remain with increasing sample throughput, enabling sample preparation, minimizing errors, and with improving data analysis.
This webinar provides the audience with an overview of the developments in NGS technologies, with an emphasis on the challenges that are routinely encountered at various stages in the sequencing and analysis of samples. It offers detailed information on the specific challenges associated with sample preparation and the benefits of using automation to alleviate some of the bottlenecks. The webinar features viewpoints expressed by three experts in the field, who share examples from their laboratories on how to effectively adopt and utilize automation for NGS applications.

What will be covered:

• Overview of NGS technologies and potential challenges in their adoption and use
• Tackling challenges associated specifically with sample prep for NGS
• Effective use of automation for alleviating some of the bottlenecks in sequencing
• Ways to increase and improve the sample throughput in sequencing
• Use and creation of high-diversity sequencing libraries
• Application of automated NGS platforms in areas like cancer genetics and CNS research
• Overview of targeted resequencing applications including effective whole exon sequencing, indexed/barcoded resequencing of small regions, automated targeted resequencing

Who will benefit from attending:

• Scientists involved in pharmaceutical/biotechnology R&D and clinical services
• Scientists keen to learn more about the use and adoption of NGS technologies
• Scientists and clinicians active in biomarker research
• Scientists looking to use sequencing for oncology and CNS research

Panelists include

• Shawn Levy, Ph.D., Faculty Investigator, HudsonAlpha Institute for Biotechnology
• Brian Minie, Ph.D., Broad Institute of MIT and Harvard
• Emily Leproust, Ph.D., Director, Applications and Chemistry R&D, Genomics, Agilent Technology

John Sterling, Editor in Chief, Genetic Engineering & Biotechnology News, will be the host of this webinar.   A live Q&A session will follow the presentations, offering you a chance to pose questions to our expert panelists.