PAVFinder

PAVFinder is a bioinformatics software tool for detecting structural variants in genomic data. It is part of the Fusion-Bloom pipeline, which is designed to identify gene fusion events in cancer samples using RNA sequencing (RNA-seq) data. PAVFinder leverages assembly-based structural variant calling technologies to contribute to Fusion-Bloom's sensitive and specific detection of gene fusions.

Topic

RNA-Seq;Sequence assembly;Transcriptomics;Gene transcripts;Biomarkers

Detail

  • Operation: De-novo assembly;Variant calling;Transcriptome assembly

  • Software interface: Command-line interface

  • Language: Python

  • License: GNU General Public License, version 3

  • Cost: Free of charge with restrictions

  • Version name: -

  • Credit: Genome Canada, Genome BC, National Institutes of Health, Natural Sciences and Engineering Research Council of Canada.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: Stable

Publications

  • Fusion-Bloom: fusion detection in assembled transcriptomes.
  • Chiu R, et al. Fusion-Bloom: fusion detection in assembled transcriptomes. Fusion-Bloom: fusion detection in assembled transcriptomes. 2020; 36:2256-2257. doi: 10.1093/bioinformatics/btz902
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ902
  • PMID: 31790154
  • PMC: PMC7141844

Download and documentation

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