FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2895547856> ?p ?o ?g. }

• W2895547856 abstract "Abstract Long read sequencing technologies such as Oxford Nanopore can greatly de-crease the complexity of de novo genome assembly and large structural variation iden-tification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. Many methods for resolving these errors require access to reference genomes, high-fidelity short reads, or reference genomes, which are often not available. De novo error correction modules are available, often as part of assembly tools, but large-scale errors still remain in resulting assemblies, motivating further innovation in this area. We developed a novel Convolutional Neu-ral Network (CNN) based method, called MiniScrub, for de novo identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments. MiniScrub first generates read-to-read alignments by MiniMap, then encodes the alignments into images, and finally builds CNN models to predict low-quality segments that could be scrubbed based on a customized quality cutoff. Applying MiniScrub to real world con-trol datasets under several different parameters, we show that it robustly improves read quality. Compared to raw reads, de novo genome assembly with scrubbed reads pro-duces many fewer mis-assemblies and large indel errors. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub" @default.
• W2895547856 created "2018-10-12" @default.
• W2895547856 creator A5046597133 @default.
• W2895547856 creator A5069883998 @default.
• W2895547856 creator A5080266778 @default.
• W2895547856 creator A5082270383 @default.
• W2895547856 date "2018-10-03" @default.
• W2895547856 modified "2023-09-24" @default.
• W2895547856 title "MiniScrub: de novo long read scrubbing using approximate alignment and deep learning" @default.
• W2895547856 cites W1920720327 @default.
• W2895547856 cites W1974640383 @default.
• W2895547856 cites W1983403167 @default.
• W2895547856 cites W2008971253 @default.
• W2895547856 cites W2082825869 @default.
• W2895547856 cites W2097205777 @default.
• W2895547856 cites W2107772251 @default.
• W2895547856 cites W2131271579 @default.
• W2895547856 cites W2136899396 @default.
• W2895547856 cites W2139437267 @default.
• W2895547856 cites W2144560237 @default.
• W2895547856 cites W2151674273 @default.
• W2895547856 cites W2157888653 @default.
• W2895547856 cites W2160177274 @default.
• W2895547856 cites W2168546919 @default.
• W2895547856 cites W2189047836 @default.
• W2895547856 cites W2194172909 @default.
• W2895547856 cites W2195724570 @default.
• W2895547856 cites W2317495605 @default.
• W2895547856 cites W2337261418 @default.
• W2895547856 cites W2525711135 @default.
• W2895547856 cites W2755804176 @default.
• W2895547856 cites W2919115771 @default.
• W2895547856 cites W2950354111 @default.
• W2895547856 cites W2951278111 @default.
• W2895547856 cites W344138311 @default.
• W2895547856 cites W4254680853 @default.
• W2895547856 doi "https://doi.org/10.1101/433573" @default.
• W2895547856 hasPublicationYear "2018" @default.
• W2895547856 type Work @default.
• W2895547856 sameAs 2895547856 @default.
• W2895547856 citedByCount "2" @default.
• W2895547856 countsByYear W28955478562019 @default.
• W2895547856 countsByYear W28955478562023 @default.
• W2895547856 crossrefType "posted-content" @default.
• W2895547856 hasAuthorship W2895547856A5046597133 @default.
• W2895547856 hasAuthorship W2895547856A5069883998 @default.
• W2895547856 hasAuthorship W2895547856A5080266778 @default.
• W2895547856 hasAuthorship W2895547856A5082270383 @default.
• W2895547856 hasBestOaLocation W28955478561 @default.
• W2895547856 hasConcept C104317684 @default.
• W2895547856 hasConcept C108583219 @default.
• W2895547856 hasConcept C11413529 @default.
• W2895547856 hasConcept C119054055 @default.
• W2895547856 hasConcept C124101348 @default.
• W2895547856 hasConcept C126513998 @default.
• W2895547856 hasConcept C127413603 @default.
• W2895547856 hasConcept C135763542 @default.
• W2895547856 hasConcept C141231307 @default.
• W2895547856 hasConcept C141795571 @default.
• W2895547856 hasConcept C150194340 @default.
• W2895547856 hasConcept C153209595 @default.
• W2895547856 hasConcept C154945302 @default.
• W2895547856 hasConcept C162317418 @default.
• W2895547856 hasConcept C18949551 @default.
• W2895547856 hasConcept C192953774 @default.
• W2895547856 hasConcept C199360897 @default.
• W2895547856 hasConcept C2776459999 @default.
• W2895547856 hasConcept C2777904410 @default.
• W2895547856 hasConcept C2778858076 @default.
• W2895547856 hasConcept C34736171 @default.
• W2895547856 hasConcept C41008148 @default.
• W2895547856 hasConcept C42360764 @default.
• W2895547856 hasConcept C54355233 @default.
• W2895547856 hasConcept C57273362 @default.
• W2895547856 hasConcept C70721500 @default.
• W2895547856 hasConcept C76155785 @default.
• W2895547856 hasConcept C86803240 @default.
• W2895547856 hasConceptScore W2895547856C104317684 @default.
• W2895547856 hasConceptScore W2895547856C108583219 @default.
• W2895547856 hasConceptScore W2895547856C11413529 @default.
• W2895547856 hasConceptScore W2895547856C119054055 @default.
• W2895547856 hasConceptScore W2895547856C124101348 @default.
• W2895547856 hasConceptScore W2895547856C126513998 @default.
• W2895547856 hasConceptScore W2895547856C127413603 @default.
• W2895547856 hasConceptScore W2895547856C135763542 @default.
• W2895547856 hasConceptScore W2895547856C141231307 @default.
• W2895547856 hasConceptScore W2895547856C141795571 @default.
• W2895547856 hasConceptScore W2895547856C150194340 @default.
• W2895547856 hasConceptScore W2895547856C153209595 @default.
• W2895547856 hasConceptScore W2895547856C154945302 @default.
• W2895547856 hasConceptScore W2895547856C162317418 @default.
• W2895547856 hasConceptScore W2895547856C18949551 @default.
• W2895547856 hasConceptScore W2895547856C192953774 @default.
• W2895547856 hasConceptScore W2895547856C199360897 @default.
• W2895547856 hasConceptScore W2895547856C2776459999 @default.
• W2895547856 hasConceptScore W2895547856C2777904410 @default.
• W2895547856 hasConceptScore W2895547856C2778858076 @default.
• W2895547856 hasConceptScore W2895547856C34736171 @default.
• W2895547856 hasConceptScore W2895547856C41008148 @default.
• W2895547856 hasConceptScore W2895547856C42360764 @default.

• next