iSeqTools Workshop at ASHG 2014


 iSeqTools to Demistify the Cloud and Genomics Analysis for Researchers Seeking Ways to Analyze High-Throughput DNA Sequencing Data


This workshop is organized and will be presented by Gabor Marth (Boston College), Goncalo Abecasis (University of Michigan), Ewa Deelman (University of Southern California), Li Ding (Washington University), Bob Handsaker (Harvard Medical School), Ali Torkamani (Scripps Institute), and Geraldine Van der Auwera (Broad Institute).

Few laboratories have the computational expertise and infrastructure necessary to accurately process and analyze the tremendous amount of data produced by high-throughput sequencing. The NHGRI iSeqTools consortium ( provides open “researcher friendly” solutions for variant calling, structural variation, RNA-seq, annotation, and interpretation in professional-grade genomic analysis workflows. Our workshop will consist of three parts. First, we will provide an overview of the “universe” of tools available through the iSeqTools network, highlighting how these tools can be used to gain new biological insights. Second, we will showcase two specific areas of great interest to the genomic community. (1) INDEL variant detection.

While SNP detection is perceived as solved, INDEL detection is much less mature. iSeqTools has a number of tools and pipelines for this purpose, and we will showcase effective workflows for both germline and somatic INDEL detection, including both mapping and de novo assembly based methods. (2) Cloud-based sequence analysis. Use of the cloud is increasingly important, but many users find it very difficult to use available systems on commercial clouds. We will showcase a number of iSeqTools examples to inform genomic scientists, and we seek to “de-mistify” genome analysis on the cloud. A panel discussion for Q&A will conclude.



The presentations for the various talks presented at the workshop are available here

  1. Introduction to iSeqTools workshop by Gabor Marth
  2. GenomeVIP:  A Genomics Analysis Pipeline for Cloud Computing with Germline and Somatic Calling on Amazon’s Cloud by R Jay Mashl
  3. Genome STRiP by Bob Handsaker
  4. gkno variant calling by Alistair Ward
  5. gotCloud by Mary Kate Wing
  6. Cloud Implementation of GT-FAR (Genome and Transcriptome-Free Analysis of RNA-Seq) by Karan Vahi
  7. Scripps Genome adviser by Galina Erikson