A Practical Evaluation of Next Generation Sequencing & Molecular Cloning Software

Research biologists increasingly face the arduous process of assessing and implementing a combination of freeware, commercial software, and web services for the management and analysis of data from high-throughput experiments. Laboratories can spend a remarkable amount of their research budgets on software, data analysis, and data management systems. The National Institutes of Health (NIH) and the National Science Foundation (NSF) have emphasized the need for contemporary software to be well-documented, interoperable, and extensible. However, laboratories often invest significant resources for personnel to build bespoke bioinformatics tools. This can have a marked impact on productivity and ROI, because these software tools often do not perform the way needed or hidden costs arise unexpectedly because of inefficiencies in the software. In this poster, we present a framework that Biomatters developed as a practical evaluation process to assist core facility managers and principal investigators to determine the best tools for DNA/RNA/protein sequence analysis and molecular cloning. The evaluation was performed on commercial & open source software packages using six criteria: 1) user interface, 2) data management, 3) data analysis, 4) feature availability, 5) extensibility, and 6) support. Thirteen software packages were evaluated (six commercial and seven free packages) using our six-tiered framework. This framework is useful for efficiently discriminating the strengths and weaknesses of the various packages, standardizes this process, and is helpful in reducing the amount of time spent on the evaluation process.