Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment

  • N. Medina-MedinaEmail author
  • A. Broka
  • S. Lacey
  • H. Lin
  • E. S. Klings
  • C. T. Baldwin
  • M. H. Steinberg
  • P. Sebastiani
Conference paper
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 154)


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.


RNA-Seq high-throughput sequencing short reads alignment ELAND BWA and Bowtie 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • N. Medina-Medina
    • 1
    Email author
  • A. Broka
    • 2
  • S. Lacey
    • 3
  • H. Lin
    • 4
  • E. S. Klings
    • 4
  • C. T. Baldwin
    • 4
  • M. H. Steinberg
    • 4
  • P. Sebastiani
    • 3
  1. 1.Department L.S.I, Technical School of Computer and Telecommunications EngineeringUniversity of GranadaGranadaSpain
  2. 2.Boston University LinGA Computing ResourceBostonUSA
  3. 3.Department of BiostatisticsBoston University School of Public HealthBostonUSA
  4. 4.Department of MedicineBoston University School of MedicineBostonUSA

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