ReadTools: A universal toolkit for handling sequence data from different sequencing platforms

Sequencing whole genomes has become a standard research tool in many disciplines including Molecular Ecology, but the rapid technological advances in combination with several competing platforms have resulted in a confusing diversity of formats. This lack of standard formats causes several problems, such as undocumented preprocessing steps or the loss of information in downstream software tools, which do not account for the specifics of the different available formats. ReadTools is an open-source Java toolkit designed to standardize and preprocess read data from different platforms. It manages FASTQ- and SAM-formatted inputs while dealing with platform-specific peculiarities and provides a standard SAM compliant output. The code and executable are available at https://github.com/magicDGS/ReadTools.