BiSpark

The software tool BiSpark is a scalable and efficient bisulfite aligner designed for processing large volumes of bisulfite sequencing data. BiSpark is implemented over the Apache Spark, a memory optimized distributed data processing framework, and is designed to support redistribution of imbalanced data to minimize delays on large-scale distributed environment. Experimental results show that BiSpark outperforms other state-of-the-art bisulfite sequencing aligners in terms of alignment speed and scalability, while providing highly consistent and comparable mapping results.

Topic

Aggregation;Read mapping;Bisulfite mapping

Detail

  • Operation: -

  • Software interface: Command-line user inteface

  • Language: Python

  • License: Not stated

  • Cost: Free

  • Version name: -

  • Credit: The National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP; Ministry of Science, ICT & Future Planning), Basic Science Research Program through the NRF funded by the Ministry of Education, the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), the Ministry of Health & Welfare, Republic of Korea, the Sookmyung Women’s University Research Grants.

  • Input: FASTA

  • Output: -

  • Contact: dane2522@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data.
  • Soe S, et al. BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data. BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data. 2018; 19:472. doi: 10.1186/s12859-018-2498-2
  • https://doi.org/10.1186/s12859-018-2498-2
  • PMID: 30526492
  • PMC: PMC6288881

Download and documentation

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