ViraPipe

ViraPipe is an Apache Spark-based scalable pipeline to analyze metagenomes using Next Generation Sequencing (NGS) datasets, adjusted for mining virus-related genomes. The ViraPipe combines BWA-MEM read aligner, MegaHit De novo assembler, and BLAST and HMMER3 sequence search tools.

Topic

Metagenomics;NGS;Sequence analysis

Detail

  • Operation: Sequence analysis;Sequence clustering;Virulence prediction

  • Software interface: Command-line user interface

  • Language: Java

  • License: The MIT licence

  • Cost: Free

  • Version name: 0.9

  • Credit: The Nordic Information for Action eScience Center (NIASC), Swedish strategic research foundation excellence project in biomarker research (BRIGHT), Academy of Finland project Advanced Parallel Testing and Verification Methods for Distributed Systems (APTV), and Helsinki Institute for Information Technology program Foundations of Computational Health (FCHealth).

  • Input: -

  • Output: -

  • Contact: ilari.maarala@aalto.fi

  • Collection: -

  • Maturity: Emerging

Publications

  • ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.
  • Maarala AI, Bzhalava Z, Dillner J, Heljanko K, Bzhalava D. ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads. Bioinformatics. 2018 Mar 15;34(6):928-935.
  • https://doi.org/10.1093/bioinformatics/btx702
  • PMID: 29106455
  • PMC: -

Download and documentation

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