FaNDOM

FaNDOM is a software tool to harness the capabilities of optical mapping (OM), a technique that offers single-molecule readouts of fluorescently labeled sequence motifs on long DNA fragments with nucleotide-level precision. The development of microfluidic technologies has enabled the generation of long OM data at a lower cost, presenting a valuable opportunity for advancements in genomic research. FaNDOM is crafted to optimize the analysis of this data, addressing the need for efficient and accurate tools capable of interpreting the complex information OM provides.

By focusing on the unique advantages of OM, including its ability to produce long-read data that complements and enhances traditional genomic sequencing techniques.

Topic

Mapping;Structural variation;Oncology;Sequence assembly;Structure analysis

Detail

  • Operation: Scaffolding;Variant calling;Mapping;Splitting

  • Software interface: Command-line interface

  • Language: Python,C++

  • License: Other

  • Cost: Free

  • Version name: -

  • Credit: NIH.

  • Input: -

  • Output: -

  • Contact: Vineet Bafna vbafna@ucsd.edu

  • Collection: -

  • Maturity: -

Publications

  • FaNDOM: Fast nested distance-based seeding of optical maps.
  • Raeisi Dehkordi S, et al. FaNDOM: Fast nested distance-based seeding of optical maps. FaNDOM: Fast nested distance-based seeding of optical maps. 2021; 2:100248. doi: 10.1016/j.patter.2021.100248
  • https://doi.org/10.1016/J.PATTER.2021.100248
  • PMID: 34027500
  • PMC: PMC8134938

Download and documentation

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