Matches in SemOpenAlex for { <https://semopenalex.org/work/W2100076391> ?p ?o ?g. }
Showing items 1 to 96 of
96
with 100 items per page.
- W2100076391 abstract "Data from large Next Generation Sequencing (NGS) experiments present challenges both in terms of costs associated with storage and in time required for file transfer. It is sometimes possible to store only a summary relevant to particular applications, but generally it is desirable to keep all information needed to revisit experimental results in the future. Thus, the need for efficient lossless compression methods for NGS reads arises. It has been shown that NGS-specific compression schemes can improve results over generic compression methods, such as the Lempel-Ziv algorithm, Burrows-Wheeler transform, or Arithmetic Coding. When a reference genome is available, effective compression can be achieved by first aligning the reads to the reference genome, and then encoding each read using the alignment position combined with the differences in the read relative to the reference. These reference-based methods have been shown to compress better than reference-free schemes, but the alignment step they require demands several hours of CPU time on a typical dataset, whereas reference-free methods can usually compress in minutes.We present a new approach that achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress. In contrast to reference-based methods that first align reads to the genome, we hash all reads into Bloom filters to encode, and decode by querying the same Bloom filters using read-length subsequences of the reference genome. Further compression is achieved by using a cascade of such filters.Our method, called BARCODE, runs an order of magnitude faster than reference-based methods, while compressing an order of magnitude better than reference-free methods, over a broad range of sequencing coverage. In high coverage (50-100 fold), compared to the best tested compressors, BARCODE saves 80-90% of the running time while only increasing space slightly." @default.
- W2100076391 created "2016-06-24" @default.
- W2100076391 creator A5026380660 @default.
- W2100076391 creator A5038806020 @default.
- W2100076391 creator A5050273239 @default.
- W2100076391 date "2014-09-01" @default.
- W2100076391 modified "2023-10-07" @default.
- W2100076391 title "Fast lossless compression via cascading Bloom filters" @default.
- W2100076391 cites W2051929999 @default.
- W2100076391 cites W2092880969 @default.
- W2100076391 cites W2110114082 @default.
- W2100076391 cites W2111044311 @default.
- W2100076391 cites W2119284644 @default.
- W2100076391 cites W2131106408 @default.
- W2100076391 cites W2159084616 @default.
- W2100076391 cites W2163584430 @default.
- W2100076391 cites W2166588423 @default.
- W2100076391 cites W2170551349 @default.
- W2100076391 cites W2179064901 @default.
- W2100076391 cites W2179933869 @default.
- W2100076391 doi "https://doi.org/10.1186/1471-2105-15-s9-s7" @default.
- W2100076391 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4168706" @default.
- W2100076391 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/25252952" @default.
- W2100076391 hasPublicationYear "2014" @default.
- W2100076391 type Work @default.
- W2100076391 sameAs 2100076391 @default.
- W2100076391 citedByCount "23" @default.
- W2100076391 countsByYear W21000763912015 @default.
- W2100076391 countsByYear W21000763912016 @default.
- W2100076391 countsByYear W21000763912017 @default.
- W2100076391 countsByYear W21000763912018 @default.
- W2100076391 countsByYear W21000763912019 @default.
- W2100076391 countsByYear W21000763912020 @default.
- W2100076391 countsByYear W21000763912022 @default.
- W2100076391 countsByYear W21000763912023 @default.
- W2100076391 crossrefType "journal-article" @default.
- W2100076391 hasAuthorship W2100076391A5026380660 @default.
- W2100076391 hasAuthorship W2100076391A5038806020 @default.
- W2100076391 hasAuthorship W2100076391A5050273239 @default.
- W2100076391 hasBestOaLocation W21000763911 @default.
- W2100076391 hasConcept C104317684 @default.
- W2100076391 hasConcept C11413529 @default.
- W2100076391 hasConcept C125411270 @default.
- W2100076391 hasConcept C141231307 @default.
- W2100076391 hasConcept C147224247 @default.
- W2100076391 hasConcept C153338461 @default.
- W2100076391 hasConcept C154945302 @default.
- W2100076391 hasConcept C175732694 @default.
- W2100076391 hasConcept C192953774 @default.
- W2100076391 hasConcept C38652104 @default.
- W2100076391 hasConcept C41008148 @default.
- W2100076391 hasConcept C55493867 @default.
- W2100076391 hasConcept C66746571 @default.
- W2100076391 hasConcept C78548338 @default.
- W2100076391 hasConcept C81081738 @default.
- W2100076391 hasConcept C86803240 @default.
- W2100076391 hasConcept C99138194 @default.
- W2100076391 hasConceptScore W2100076391C104317684 @default.
- W2100076391 hasConceptScore W2100076391C11413529 @default.
- W2100076391 hasConceptScore W2100076391C125411270 @default.
- W2100076391 hasConceptScore W2100076391C141231307 @default.
- W2100076391 hasConceptScore W2100076391C147224247 @default.
- W2100076391 hasConceptScore W2100076391C153338461 @default.
- W2100076391 hasConceptScore W2100076391C154945302 @default.
- W2100076391 hasConceptScore W2100076391C175732694 @default.
- W2100076391 hasConceptScore W2100076391C192953774 @default.
- W2100076391 hasConceptScore W2100076391C38652104 @default.
- W2100076391 hasConceptScore W2100076391C41008148 @default.
- W2100076391 hasConceptScore W2100076391C55493867 @default.
- W2100076391 hasConceptScore W2100076391C66746571 @default.
- W2100076391 hasConceptScore W2100076391C78548338 @default.
- W2100076391 hasConceptScore W2100076391C81081738 @default.
- W2100076391 hasConceptScore W2100076391C86803240 @default.
- W2100076391 hasConceptScore W2100076391C99138194 @default.
- W2100076391 hasIssue "S9" @default.
- W2100076391 hasLocation W21000763911 @default.
- W2100076391 hasLocation W21000763912 @default.
- W2100076391 hasLocation W21000763913 @default.
- W2100076391 hasLocation W21000763914 @default.
- W2100076391 hasOpenAccess W2100076391 @default.
- W2100076391 hasPrimaryLocation W21000763911 @default.
- W2100076391 hasRelatedWork W1571468614 @default.
- W2100076391 hasRelatedWork W2005009257 @default.
- W2100076391 hasRelatedWork W2100076391 @default.
- W2100076391 hasRelatedWork W2134574137 @default.
- W2100076391 hasRelatedWork W2329237514 @default.
- W2100076391 hasRelatedWork W2349573707 @default.
- W2100076391 hasRelatedWork W2366609716 @default.
- W2100076391 hasRelatedWork W2754376138 @default.
- W2100076391 hasRelatedWork W3162685931 @default.
- W2100076391 hasRelatedWork W2311146512 @default.
- W2100076391 hasVolume "15" @default.
- W2100076391 isParatext "false" @default.
- W2100076391 isRetracted "false" @default.
- W2100076391 magId "2100076391" @default.
- W2100076391 workType "article" @default.