Manipulation of FASTQ data with Galaxy.

SUMMARY: Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine all the way through the quality filtering steps. AVAILABILITY AND IMPLEMENTATION: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Two short movies that highlight the functionality of tools described in this manuscript as well as results from testing components of this tool suite against a set of previously published files are available at http://usegalaxy.org/u/dan/p/fastq

Integrating diverse databases into an unified analysis framework: a Galaxy approach.

Recent technological advances have lead to the ability to generate large amounts of data for model and non-model organisms. Whereas, in the past, there have been a relatively small number of central repositories that serve genomic data, an increasing number of distinct specialized data repositories and resources have been established. Here, we describe a generic approach that provides for the integration of a diverse spectrum of data resources into a unified analysis framework, Galaxy (http://usegalaxy.org). This approach allows the simplified coupling of external data resources with the data analysis tools available to Galaxy users, while leveraging the native data mining facilities of the external data resources. DATABASE URL: http://usegalaxy.org.