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Published in:
2012 | OriginalPaper | Chapter
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment
Authors : N. Medina-Medina, A. Broka, S. Lacey, H. Lin, E. S. Klings, C. T. Baldwin, M. H. Steinberg, P. Sebastiani
Published in: 6th International Conference on Practical Applications of Computational Biology & Bioinformatics
Publisher: Springer Berlin Heidelberg
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High-throughput sequencing technologies are a significant innovation that can contribute to important advances in genetic research. In recent years, many algorithms have been developed to align the large number of short nucleotide sequences generated by these technologies. Choosing within the available alignment algorithms is difficult; to assist this decision we evaluate several algorithms for the mapping of RNA-Seq data. The comparison was completed in two phases. An initial phase narrowed down the comparison to the three algorithms implemented in the tools: ELAND, Bowtie and BWA. A second phase compared the tools in terms of runtime, alignment coverage and process control.