Fuzzy set intersection based paired-end short-read alignment Article Swipe
William J. Bolosky
,
Arun Subramaniyan
,
Matei Zaharia
,
Ravi Pandya
,
Taylor Sittler
,
David S. Patterson
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1136395/v1
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1136395/v1
Much genomic data comes in the form of paired-end reads: two reads that represent genetic material with a small gap between. We present a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. This algorithm is often much faster and produces alignments that result in variant calls having roughly the same concordance as the best competing aligners.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-1136395/v1
- https://www.researchsquare.com/article/rs-1136395/latest.pdf
- OA Status
- gold
- Cited By
- 4
- References
- 63
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4226073983
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Raw OpenAlex JSON
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https://openalex.org/W4226073983Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-1136395/v1Digital Object Identifier
- Title
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Fuzzy set intersection based paired-end short-read alignmentWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
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2021-12-16Full publication date if available
- Authors
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William J. Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, David S. PattersonList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-1136395/v1Publisher landing page
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https://www.researchsquare.com/article/rs-1136395/latest.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://www.researchsquare.com/article/rs-1136395/latest.pdfDirect OA link when available
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Intersection (aeronautics), Set (abstract data type), Computer science, Algorithm, Fuzzy logic, Artificial intelligence, Pattern recognition (psychology), Engineering, Aerospace engineering, Programming languageTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2, 2024: 1, 2022: 1Per-year citation counts (last 5 years)
- References (count)
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63Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.comes | 4 |
| abstract_inverted_index.often | 50 |
| abstract_inverted_index.read. | 46 |
| abstract_inverted_index.reads | 12, 30 |
| abstract_inverted_index.small | 19 |
| abstract_inverted_index.faster | 52 |
| abstract_inverted_index.having | 61 |
| abstract_inverted_index.reads: | 10 |
| abstract_inverted_index.result | 57 |
| abstract_inverted_index.fuzzily | 36 |
| abstract_inverted_index.genetic | 15 |
| abstract_inverted_index.genomic | 2 |
| abstract_inverted_index.present | 23 |
| abstract_inverted_index.roughly | 62 |
| abstract_inverted_index.variant | 59 |
| abstract_inverted_index.aligning | 28 |
| abstract_inverted_index.between. | 21 |
| abstract_inverted_index.material | 16 |
| abstract_inverted_index.produces | 54 |
| abstract_inverted_index.algorithm | 26, 48 |
| abstract_inverted_index.aligners. | 70 |
| abstract_inverted_index.alignment | 42 |
| abstract_inverted_index.candidate | 41 |
| abstract_inverted_index.competing | 69 |
| abstract_inverted_index.locations | 43 |
| abstract_inverted_index.represent | 14 |
| abstract_inverted_index.alignments | 55 |
| abstract_inverted_index.paired-end | 9 |
| abstract_inverted_index.concordance | 65 |
| abstract_inverted_index.intersecting | 37 |
| abstract_inverted_index.simultaneously | 34 |
| abstract_inverted_index.<title>Abstract</title> | 0 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 89 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 6 |
| citation_normalized_percentile.value | 0.52657091 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |