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Spark Basic Local Alignment Search Tool SparkBLAST

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Allows to parallelize and manage the execution of BLAST either on dedicated clusters or cloud environments. SparkBLAST is based on cloud computing for the provisioning of computational resources and uses Apache Spark as the coordination framework. It was evaluated on both Google and Microsoft Azure Clouds, for several configurations and dataset sizes. The tool is able to achieve, in average, a maximum speedup of 41.78, reducing the execution time from 28,983 s in a single node, to 693 s in 64 nodes.

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SparkBLAST versioning

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SparkBLAST classification

SparkBLAST specifications

Software type:
Application/Script
Restrictions to use:
None
Programming languages:
Java, Scala, Shell (Bash)
Computer skills:
Advanced
Interface:
Command line interface
Operating system:
Unix/Linux
License:
BSD 3-clause “New” or “Revised” License
Stability:
Stable
Maintained:
Yes

SparkBLAST support

Maintainer

  • Fabricio da Silva <>

Credits

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Publications

Institution(s)

Computer Science Department, Federal University of São Carlos, São Carlos, Brazil; LBCS-IOC, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; PROCC, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

Funding source(s)

Supported by Google, Microsoft Research, CAPES, CNPq, FAPERJ and IFSULDEMINAS; and CNPq (Contract Number 305032/2015-1).

Link to literature

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