Matches in SemOpenAlex for { <https://semopenalex.org/work/W4220807510> ?p ?o ?g. }
Showing items 1 to 71 of
71
with 100 items per page.
- W4220807510 abstract "Motivation: The quality of reference genomes critically affects analyses of next generation sequencing experiments. During the construction of the reference genome, contigs are organized into their underlying chromosomes in the scaffolding step. Historically, the quality of scaffolding software has been difficult to evaluate in a systematic and quantitative fashion. To this end, we identified genomic edit distance as a compelling method for evaluating the quality of a scaffold. Results: We present Edison, a Python implementation of the Double Cut and Join (DCJ) edit distance algorithm. Edison calculates the overall accuracy of a given scaffold using a reference genome and also provides scores for characterizing different aspects of the scaffolding accuracy, including grouping, ordering, and orientation. All metrics are calculated on a length-weighted basis, which rewards the correct placement of longer contigs over shorter ones. By creating 1000 random assemblies of the S. cerevisiae genome, we show that our scaffolding accuracy provides a more reliable metric than the commonly used metric, N50. Edison can be used to benchmark new scaffolding algorithms, providing insights into the strengths and weaknesses of each approach. Availability and Implementation: Edison is available under an MIT license at https://github.com/Noble- Lab/edison." @default.
- W4220807510 created "2022-04-03" @default.
- W4220807510 creator A5043469393 @default.
- W4220807510 creator A5049054709 @default.
- W4220807510 creator A5049689507 @default.
- W4220807510 creator A5057375933 @default.
- W4220807510 date "2022-03-28" @default.
- W4220807510 modified "2023-09-27" @default.
- W4220807510 title "Edison: measuring scaffolding accuracy with edit distance" @default.
- W4220807510 doi "https://doi.org/10.1101/2022.03.25.484952" @default.
- W4220807510 hasPublicationYear "2022" @default.
- W4220807510 type Work @default.
- W4220807510 citedByCount "0" @default.
- W4220807510 crossrefType "posted-content" @default.
- W4220807510 hasAuthorship W4220807510A5043469393 @default.
- W4220807510 hasAuthorship W4220807510A5049054709 @default.
- W4220807510 hasAuthorship W4220807510A5049689507 @default.
- W4220807510 hasAuthorship W4220807510A5057375933 @default.
- W4220807510 hasBestOaLocation W42208075101 @default.
- W4220807510 hasConcept C104317684 @default.
- W4220807510 hasConcept C11413529 @default.
- W4220807510 hasConcept C124101348 @default.
- W4220807510 hasConcept C127413603 @default.
- W4220807510 hasConcept C13280743 @default.
- W4220807510 hasConcept C141231307 @default.
- W4220807510 hasConcept C176217482 @default.
- W4220807510 hasConcept C185798385 @default.
- W4220807510 hasConcept C199360897 @default.
- W4220807510 hasConcept C205649164 @default.
- W4220807510 hasConcept C21547014 @default.
- W4220807510 hasConcept C2777904410 @default.
- W4220807510 hasConcept C41008148 @default.
- W4220807510 hasConcept C519991488 @default.
- W4220807510 hasConcept C55493867 @default.
- W4220807510 hasConcept C59582021 @default.
- W4220807510 hasConcept C86803240 @default.
- W4220807510 hasConcept C89429830 @default.
- W4220807510 hasConceptScore W4220807510C104317684 @default.
- W4220807510 hasConceptScore W4220807510C11413529 @default.
- W4220807510 hasConceptScore W4220807510C124101348 @default.
- W4220807510 hasConceptScore W4220807510C127413603 @default.
- W4220807510 hasConceptScore W4220807510C13280743 @default.
- W4220807510 hasConceptScore W4220807510C141231307 @default.
- W4220807510 hasConceptScore W4220807510C176217482 @default.
- W4220807510 hasConceptScore W4220807510C185798385 @default.
- W4220807510 hasConceptScore W4220807510C199360897 @default.
- W4220807510 hasConceptScore W4220807510C205649164 @default.
- W4220807510 hasConceptScore W4220807510C21547014 @default.
- W4220807510 hasConceptScore W4220807510C2777904410 @default.
- W4220807510 hasConceptScore W4220807510C41008148 @default.
- W4220807510 hasConceptScore W4220807510C519991488 @default.
- W4220807510 hasConceptScore W4220807510C55493867 @default.
- W4220807510 hasConceptScore W4220807510C59582021 @default.
- W4220807510 hasConceptScore W4220807510C86803240 @default.
- W4220807510 hasConceptScore W4220807510C89429830 @default.
- W4220807510 hasLocation W42208075101 @default.
- W4220807510 hasOpenAccess W4220807510 @default.
- W4220807510 hasPrimaryLocation W42208075101 @default.
- W4220807510 hasRelatedWork W1485630101 @default.
- W4220807510 hasRelatedWork W2020006618 @default.
- W4220807510 hasRelatedWork W2118451750 @default.
- W4220807510 hasRelatedWork W2152989354 @default.
- W4220807510 hasRelatedWork W2498017833 @default.
- W4220807510 hasRelatedWork W2529681551 @default.
- W4220807510 hasRelatedWork W2887749901 @default.
- W4220807510 hasRelatedWork W3147774920 @default.
- W4220807510 hasRelatedWork W3159163876 @default.
- W4220807510 hasRelatedWork W4220807510 @default.
- W4220807510 isParatext "false" @default.
- W4220807510 isRetracted "false" @default.
- W4220807510 workType "article" @default.