Matches in SemOpenAlex for { <https://semopenalex.org/work/W4387346476> ?p ?o ?g. }
Showing items 1 to 97 of
97
with 100 items per page.
- W4387346476 abstract "The COVID-19 pandemic forever underscored the need for bio-surveillance platforms capable of rapidly detecting emerging pathogens. Oxford Nanopore Technology (ONT) couples long-read sequencing with in-field capability, opening the door to real-time, in-field biosurveillance. Though a promising technology, streaming assignment of accurate functional and taxonomic labels with nanopore reads remains challenging given: (i) individual reads can span multiple genes, (ii) individual reads may contain truncated genes and pseudogenes, (iii) the error rate of the ONT platform that may introduce frameshifts and missense errors, and (iv) the computational costs of read-by-read analysis may exceed that of in-field computational equipment. Altogether, these challenges highlight a need for novel computational approaches. To this end, we describe Seqscreen-Nano, a novel and portable computational platform focused on detecting microbial pathogens. Based on results from simulated and synthetic microbial communities, SeqScreen-Nano can identify Open Reading Frames (ORFs) across the length of raw ONT reads and then use the predicted ORFs for accurate functional characterization and taxonomic classification. SeqScreen-Nano also runs efficiently in a memory-constrained environment (less than 32GB of RAM), allowing it to be utilized in resource-limited settings. Furthermore, SeqScreen-Nano can process reads directly from the ONT MinION sequencing device, enabling streaming and in-field characterization of microbial pathogens. SeqScreen-Nano (v4.2) is available on GitLab at: https://gitlab.com/treangenlab/seqscreen" @default.
- W4387346476 created "2023-10-05" @default.
- W4387346476 creator A5017112080 @default.
- W4387346476 creator A5022447343 @default.
- W4387346476 creator A5025825738 @default.
- W4387346476 creator A5064309237 @default.
- W4387346476 creator A5072547539 @default.
- W4387346476 creator A5083401418 @default.
- W4387346476 creator A5085118545 @default.
- W4387346476 creator A5086298034 @default.
- W4387346476 creator A5080226175 @default.
- W4387346476 date "2023-09-03" @default.
- W4387346476 modified "2023-10-06" @default.
- W4387346476 title "SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens" @default.
- W4387346476 cites W2116423958 @default.
- W4387346476 cites W2616925143 @default.
- W4387346476 cites W2936556823 @default.
- W4387346476 cites W2969831762 @default.
- W4387346476 cites W3011982747 @default.
- W4387346476 cites W3012944241 @default.
- W4387346476 cites W3080270089 @default.
- W4387346476 cites W3091506611 @default.
- W4387346476 cites W3097320816 @default.
- W4387346476 cites W3128727817 @default.
- W4387346476 cites W3148149465 @default.
- W4387346476 cites W3209785727 @default.
- W4387346476 cites W4283031711 @default.
- W4387346476 cites W4283726298 @default.
- W4387346476 cites W4287578669 @default.
- W4387346476 doi "https://doi.org/10.1145/3584371.3612960" @default.
- W4387346476 hasPublicationYear "2023" @default.
- W4387346476 type Work @default.
- W4387346476 citedByCount "0" @default.
- W4387346476 crossrefType "proceedings-article" @default.
- W4387346476 hasAuthorship W4387346476A5017112080 @default.
- W4387346476 hasAuthorship W4387346476A5022447343 @default.
- W4387346476 hasAuthorship W4387346476A5025825738 @default.
- W4387346476 hasAuthorship W4387346476A5064309237 @default.
- W4387346476 hasAuthorship W4387346476A5072547539 @default.
- W4387346476 hasAuthorship W4387346476A5080226175 @default.
- W4387346476 hasAuthorship W4387346476A5083401418 @default.
- W4387346476 hasAuthorship W4387346476A5085118545 @default.
- W4387346476 hasAuthorship W4387346476A5086298034 @default.
- W4387346476 hasBestOaLocation W43873464761 @default.
- W4387346476 hasConcept C104317684 @default.
- W4387346476 hasConcept C126513998 @default.
- W4387346476 hasConcept C141231307 @default.
- W4387346476 hasConcept C149635348 @default.
- W4387346476 hasConcept C154945302 @default.
- W4387346476 hasConcept C167625842 @default.
- W4387346476 hasConcept C202444582 @default.
- W4387346476 hasConcept C2779927696 @default.
- W4387346476 hasConcept C2780513914 @default.
- W4387346476 hasConcept C2780530800 @default.
- W4387346476 hasConcept C33923547 @default.
- W4387346476 hasConcept C41008148 @default.
- W4387346476 hasConcept C47289529 @default.
- W4387346476 hasConcept C54355233 @default.
- W4387346476 hasConcept C70721500 @default.
- W4387346476 hasConcept C86803240 @default.
- W4387346476 hasConcept C9652623 @default.
- W4387346476 hasConceptScore W4387346476C104317684 @default.
- W4387346476 hasConceptScore W4387346476C126513998 @default.
- W4387346476 hasConceptScore W4387346476C141231307 @default.
- W4387346476 hasConceptScore W4387346476C149635348 @default.
- W4387346476 hasConceptScore W4387346476C154945302 @default.
- W4387346476 hasConceptScore W4387346476C167625842 @default.
- W4387346476 hasConceptScore W4387346476C202444582 @default.
- W4387346476 hasConceptScore W4387346476C2779927696 @default.
- W4387346476 hasConceptScore W4387346476C2780513914 @default.
- W4387346476 hasConceptScore W4387346476C2780530800 @default.
- W4387346476 hasConceptScore W4387346476C33923547 @default.
- W4387346476 hasConceptScore W4387346476C41008148 @default.
- W4387346476 hasConceptScore W4387346476C47289529 @default.
- W4387346476 hasConceptScore W4387346476C54355233 @default.
- W4387346476 hasConceptScore W4387346476C70721500 @default.
- W4387346476 hasConceptScore W4387346476C86803240 @default.
- W4387346476 hasConceptScore W4387346476C9652623 @default.
- W4387346476 hasFunder F4320306076 @default.
- W4387346476 hasFunder F4320332161 @default.
- W4387346476 hasFunder F4320333051 @default.
- W4387346476 hasLocation W43873464761 @default.
- W4387346476 hasOpenAccess W4387346476 @default.
- W4387346476 hasPrimaryLocation W43873464761 @default.
- W4387346476 hasRelatedWork W2521280993 @default.
- W4387346476 hasRelatedWork W2770952292 @default.
- W4387346476 hasRelatedWork W2781129742 @default.
- W4387346476 hasRelatedWork W2893909145 @default.
- W4387346476 hasRelatedWork W2950636974 @default.
- W4387346476 hasRelatedWork W2951181326 @default.
- W4387346476 hasRelatedWork W3109164186 @default.
- W4387346476 hasRelatedWork W3121387483 @default.
- W4387346476 hasRelatedWork W3198130009 @default.
- W4387346476 hasRelatedWork W4381248099 @default.
- W4387346476 isParatext "false" @default.
- W4387346476 isRetracted "false" @default.
- W4387346476 workType "article" @default.