Japan Bioinformatics Announces Study on Leading Mapping Tools for DNA Mutation Discovery

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Analyses indicate leading mapping tools do not provide similar results

Japan Bioinformatics, today announced results of a study on the impact three popular mapping tools have on the results of SNP discovery experiments and the analysis of sequence data.

Mutation discovery, especially discovery of single nucleotide polymorphisms (SNPs) is an extremely popular analysis of sequence data in many types of research, including cancer. The data from Next Generation Sequencing (NGS) devices provides a very cost-effective and convenient source of information. Additionally, the proliferation of NGS-focused data analysis tools makes this type of research easily accessible to individual researchers.

Japan Bioinformatics recently published a study, which utilizes Simbiot®, a cloud-based next generation sequencing data analysis tool, to explore the impact three popular mapping tools have on the results of SNP discovery experiments.

Bowtie, Bowtie2 and BWA mapping tools were tested using data from a human cancer panel, a human exome and Caenhorhabditis elegans whole genome. In all three cases, the results were consistent:

  • Bowtie detected the smallest number of SNPs and almost no insertions or deletions (INDELs)
  • Bowtie2 and BWA were able to detect a similar number of mutations
  • There were significant discrepancies between the SNPs detected using Bowtie2 and those detected using BWA
  • The results of INDEL analysis in the human exome data set show that 67% of the filtered, high quality INDELs were common between mutations detected using Bowtie2 and those detected using BWA genome aligners.

For the complete results of the analysis, download the white paper,

About Japan Bioinformatics
Japan Bioinformatics KK is a Tokyo-based biotechnology company specializing in software development, as well as bioinformatics and information technology services to the life science community, including biotechnology, academia, research, pharmaceutical and bio-devices organizations.

Our main product is Simbiot ®, a system for management and analysis of biological data. The application is available in single-user and private server configuration that easily integrates into client’s environment, including laboratory information management systems (LIMS), as well as custom and proprietary data formats, analytics and annotations. The system combines reliable data management, distribution, collaboration and analysis tools that support commercial and proprietary data formats with specific focus on next generation sequencing (NGS) data.

In addition to software products, Japan Bioinformatics offers, we also offer data analysis, bioinformatics and software development services. Learn more at http://www.japanbioinformatics.com.

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Boris Umylny
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