Seal is a Hadoop-based distributed short read alignment and analysis toolkit. Currently Seal includes tools for: read demultiplexing, read alignment, duplicate read removal, sorting read mappings, and calculating statistics for empirical base quality recalibration. Seal scales, easily handling TB of data.


  • short read alignment (based on BWA)
  • duplicate read identification
  • sort read mappings
  • calculate empirical base quality recalibration tables
  • fast, scalable, reliable (runs on Hadoop)

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