FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3138612847> ?p ?o ?g. }

• W3138612847 abstract "Background: Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on the ability to classify sequences based on correct decoding of these combinatorial barcodes. The probability of correct decoding is influenced by both sequence quality and the number and arrangement of barcodes. The rising complexity of experimental designs calls for a probability model that accounts for both sequencing errors and random noise, generalizes to multiple combinatorial tags, and can handle any barcoding scheme. The needs for reproducibility and community benchmark standards demand a peer-reviewed tool that preserves decoding quality scores and provides tunable control over classification confidence that balances precision and recall. Moreover, continuous improvements in sequencing throughput require a fast, parallelized and scalable implementation. Results: We developed a flexible, robustly engineered software that performs probabilistic decoding and supports arbitrarily complex barcoding designs. Pheniqs computes the full posterior decoding error probability of observed barcodes by consulting basecalling quality scores and prior distributions, and reports sequences and confidence scores in Sequence Alignment/Map (SAM) fields. The product of posteriors for multiple independent barcodes provides an overall confidence score for each read. Pheniqs achieves greater accuracy than minimum edit distance or simple maximum likelihood estimation, and it scales linearly with core count to enable the classification of >11 billion reads in 1h15m using <50 megabytes of memory. Pheniqs has been in production use for seven years in our genomics core facility. Conclusions: We introduce a computationally efficient software that implements both probabilistic and minimum distance decoders and show that decoding barcodes using posterior probabilities is more accurate than available methods. Pheniqs allows fine-tuning of decoding sensitivity using intuitive confidence thresholds and is extensible with alternative decoders and new error models. Any arbitrary arrangement of barcodes is easily configured, enabling computation of combinatorial confidence scores for any barcoding strategy. An optimized multithreaded implementation assures that Pheniqs is faster and scales better with complex barcode sets than existing tools. Support for POSIX streams and multiple sequencing formats enables easy integration with automated analysis pipelines." @default.
• W3138612847 created "2021-03-29" @default.
• W3138612847 creator A5029062123 @default.
• W3138612847 creator A5055576104 @default.
• W3138612847 creator A5071207181 @default.
• W3138612847 date "2021-03-12" @default.
• W3138612847 modified "2023-09-24" @default.
• W3138612847 title "Pheniqs 2.0: accurate, high performance Bayesian decoding and confidence estimation for combinatorial barcode indexing" @default.
• W3138612847 cites W1687449080 @default.
• W3138612847 cites W2103441770 @default.
• W3138612847 cites W2108234281 @default.
• W3138612847 cites W2132840768 @default.
• W3138612847 cites W2162667876 @default.
• W3138612847 cites W2747545374 @default.
• W3138612847 cites W2884441543 @default.
• W3138612847 cites W2921990535 @default.
• W3138612847 cites W2944073176 @default.
• W3138612847 cites W2949177718 @default.
• W3138612847 cites W2949436170 @default.
• W3138612847 cites W2950519970 @default.
• W3138612847 cites W2952229854 @default.
• W3138612847 doi "https://doi.org/10.1101/2021.03.11.434956" @default.
• W3138612847 hasPublicationYear "2021" @default.
• W3138612847 type Work @default.
• W3138612847 sameAs 3138612847 @default.
• W3138612847 citedByCount "0" @default.
• W3138612847 crossrefType "posted-content" @default.
• W3138612847 hasAuthorship W3138612847A5029062123 @default.
• W3138612847 hasAuthorship W3138612847A5055576104 @default.
• W3138612847 hasAuthorship W3138612847A5071207181 @default.
• W3138612847 hasBestOaLocation W31386128471 @default.
• W3138612847 hasConcept C111919701 @default.
• W3138612847 hasConcept C11413529 @default.
• W3138612847 hasConcept C124101348 @default.
• W3138612847 hasConcept C13280743 @default.
• W3138612847 hasConcept C154945302 @default.
• W3138612847 hasConcept C185798385 @default.
• W3138612847 hasConcept C205649164 @default.
• W3138612847 hasConcept C2776841711 @default.
• W3138612847 hasConcept C41008148 @default.
• W3138612847 hasConcept C49937458 @default.
• W3138612847 hasConcept C57273362 @default.
• W3138612847 hasConceptScore W3138612847C111919701 @default.
• W3138612847 hasConceptScore W3138612847C11413529 @default.
• W3138612847 hasConceptScore W3138612847C124101348 @default.
• W3138612847 hasConceptScore W3138612847C13280743 @default.
• W3138612847 hasConceptScore W3138612847C154945302 @default.
• W3138612847 hasConceptScore W3138612847C185798385 @default.
• W3138612847 hasConceptScore W3138612847C205649164 @default.
• W3138612847 hasConceptScore W3138612847C2776841711 @default.
• W3138612847 hasConceptScore W3138612847C41008148 @default.
• W3138612847 hasConceptScore W3138612847C49937458 @default.
• W3138612847 hasConceptScore W3138612847C57273362 @default.
• W3138612847 hasLocation W31386128471 @default.
• W3138612847 hasOpenAccess W3138612847 @default.
• W3138612847 hasPrimaryLocation W31386128471 @default.
• W3138612847 hasRelatedWork W1485630101 @default.
• W3138612847 hasRelatedWork W1988678654 @default.
• W3138612847 hasRelatedWork W2015756483 @default.
• W3138612847 hasRelatedWork W2030492936 @default.
• W3138612847 hasRelatedWork W2126742497 @default.
• W3138612847 hasRelatedWork W2151268798 @default.
• W3138612847 hasRelatedWork W2166175595 @default.
• W3138612847 hasRelatedWork W2548393475 @default.
• W3138612847 hasRelatedWork W3018808206 @default.
• W3138612847 hasRelatedWork W59016736 @default.
• W3138612847 isParatext "false" @default.
• W3138612847 isRetracted "false" @default.
• W3138612847 magId "3138612847" @default.
• W3138612847 workType "article" @default.