A package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead extends Bioconductor with tools useful in the initial stages of short-read DNA sequence analysis. Main functionalities include data input, quality assessment, data transformation and access to downstream analysis opportunities. It is an important gateway to use of Bioconductor for processing high-throughput DNA sequence data. ShortRead data structures allow convenient manipulation of data, such as filtering reads based on sequence characteristics.