Tag Archives: exome analysis

28.07.2016 | Poster about EAGLE at ECCB

A poster about the Exome Analysis GraphicaL Environment (EAGLE) was accepted for the ECCB 2016 at The Hague. Felix Mölder will present the poster there.

EAGLE: an easy-to-use web-based exome analysis environment
Christopher Schröder, Felix Mölder, Christoph Stahl and Sven Rahmann

Abstract:
High throughput exome sequencing is a widely used technology for deciphering mutations in the coding regions of a genome at relatively low cost. While bioinformatics analyses of exome sequencing data mostly agree on best practices regarding the analysis steps, called genomic variants depend on the set of parameters and applied filtering. We present EAGLE, a software that combines a best practices variant calling workflow with a web frontend. By storing the called variant information in HDF5 files (instead of SQL databases), EAGLE allows filtering and parameter tuning in almost real time. This enables iterative tuning of thresholds, or the selection of different samples for filtering by medical PIs via the web interface. The web interface presents metadata, annotations, quality control data and statistics to facilitate a comprehensive data analysis on different levels.

Poster about the EAGLE tool at University Hospital Essen Science Day 2015

Exome Analysis GraphicaL Environment (EAGLE)

Christopher Schröder, Christoph Stahl, Felix Mölder, André Janowicz, Jasmin Beygo, Marcel Martin, Sven Rahmanneagle

The Exome Analysis GraphicaL Environment (EAGLE) combines a best practices variant calling workflow, with a web frontend. By storing the called information in speficially structerd hdf5 files, EAGLE allows filtering and parameter tuning in almost real time. This enables iterative tuning of thresholds, or the selection of different samples for filtering by non computer scientists via the web interface.

Poster on Exomate at GfH 2014 in Essen

exomate-posterExomate: an easy to use exome sequencing analysis pipeline

Christopher Schröder, Johannes Köster, Christoph Stahl, Sebastian Venier, Sven Rahmann, Marcel Martin

Exomate is an exome-sequencing pipeline with a web frontend. It automates most steps needed to go from FASTQ files to variant calls, puts the calls and metadata about patients, samples, etc. into a database and then allows interactive analysis via a web frontend. It is primarily designed for easy use and has already been used in various studies [1,2,3].

[1] Martin, M. et al., 2013. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat. Genet. 45, 933–936.

[2] Czeschik, J.C. et al., 2013. Clinical and mutation data in 12 patients with the clinical diagnosis of Nager syndrome. Hum. Genet. 132, 885–898.

[3] Voigt, C., et al., 2013. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies – expanding the phenotypes associated with EFTUD2 hfg mutations.
Orphanet J Rare Dis 8, 110.