FaNDOM: Fast nested distance-based seeding of optical maps.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 34027500.
- Also identified by DOI 10.1016/j.patter.2021.100248 and PMC identifier 8134938.
- Licence recorded as CC BY-NC-ND.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
Optical mapping (OM) provides single-molecule readouts of fluorescently labeled sequence motifs on long fragments of DNA, resolved to nucleotide-level coordinates. With the advent of microfluidic technologies for analysis of DNA molecules, it is possible to inexpensively generate long OM data ( <math xmlns="http://www.w3.org/1998/Math/MathML"><mrow><mo>></mo> <mn>150</mn></mrow> </math> kbp) at high coverage. In addition to scaffolding for <i>de novo</i> assembly, OM data can be aligned to a reference genome for identification of genomic structural variants. We introduce FaNDOM (Fast Nested Distance Seeding of Optical Maps)-an optical map alignment tool that greatly reduces the search space of the alignment process. On four benchmark human datasets, FaNDOM was significantly (4-14×) faster than competing tools while maintaining comparable sensitivity and specificity. We used FaNDOM to map variants in three cancer cell lines and identified many biologically interesting structural variants, including deletions, duplications, gene fusions and gene-disrupting rearrangements. FaNDOM is publicly available at https://github.com/jluebeck/FaNDOM.