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GEM: crystal-clear DNA alignment

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The Genome Multitool (GEM) mapper rapidly and accurately provides all alignments of a read within a user-defined number of mismatches.

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Figure 1: A query sequence (center) is broken into equal-length regions.

References

  1. Li, H. & Homer, N. Brief. Bioinform. 11, 473–483 (2010).

    Article  CAS  Google Scholar 

  2. Marco-Sola, S., Sammeth, M., Guigó, R. & Ribeca, P. Nat. Methods 9, 1185–1188 (2012).

    Article  CAS  Google Scholar 

  3. Li, R. et al. Bioinformatics 25, 1966–1967 (2009).

    Article  CAS  Google Scholar 

  4. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  5. Langmead, B. & Salzberg, S.L. Nat. Methods 9, 357–359 (2012).

    Article  CAS  Google Scholar 

  6. Li, H. & Durbin, R. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  7. Alkan, C. et al. Nat. Genet. 41, 1061–1067 (2009).

    Article  CAS  Google Scholar 

  8. Li, H. & Durbin, R. Bioinformatics 26, 589–595 (2010).

    Article  Google Scholar 

  9. Alkan, C., Coe, B.P. & Eichler, E.E. Nat. Rev. Genet. 12, 363–376 (2011).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Gregory G. Faust is in the Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA.,

    Gregory G Faust

  2. Ira M. Hall is at the Center for Public Health Genomics and both are in the Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA.,

    Gregory G Faust & Ira M Hall

Authors
  1. Gregory G Faust
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  2. Ira M Hall
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Correspondence to Ira M Hall.

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The authors declare no competing financial interests.

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Faust, G., Hall, I. GEM: crystal-clear DNA alignment. Nat Methods 9, 1159–1160 (2012). https://doi.org/10.1038/nmeth.2256

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  • DOI: https://doi.org/10.1038/nmeth.2256

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