Manipulation of FASTQ data with Galaxy.

ABSTRACT

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