Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin’s approach to UMI deduplication con...

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Veröffentlicht in:	Genome Biology Jg. 20; H. 1; S. 65
Hauptverfasser:	Srivastava, Avi, Malik, Laraib, Smith, Tom, Sudbery, Ian, Patro, Rob
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London BioMed Central 27.03.2019 Springer Nature B.V BMC
Schlagworte:	Algorithms Animal Genetics and Genomics Animals Bioinformatics Biomedical and Life Sciences Cellular barcode Datasets DNA Barcoding, Taxonomic Evolutionary Biology Gene expression Gene mapping genes Genomes Genomics Human Genetics Humans Life Sciences Method Mice Microbial Genetics and Genomics nucleotide sequences pipelines Plant Genetics and Genomics Quantification Ribonucleic acid RNA sequence analysis Sequence Analysis, RNA Single-Cell Analysis Single-cell RNA-seq Software Transcription UMI deduplication Cellular barcode UMI deduplication Quantification Single-cell RNA-seq
ISSN:	1474-760X, 1474-7596, 1474-760X
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Abstract	We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin’s approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory.
AbstractList	We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin's approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory.We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin's approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory. We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin’s approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory. Abstract We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin’s approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory.
ArticleNumber	65
Author	Sudbery, Ian Srivastava, Avi Patro, Rob Malik, Laraib Smith, Tom
Author_xml	– sequence: 1 givenname: Avi surname: Srivastava fullname: Srivastava, Avi organization: Department of Computer Science, Stony Brook University – sequence: 2 givenname: Laraib surname: Malik fullname: Malik, Laraib organization: Department of Computer Science, Stony Brook University – sequence: 3 givenname: Tom surname: Smith fullname: Smith, Tom organization: Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge – sequence: 4 givenname: Ian surname: Sudbery fullname: Sudbery, Ian organization: Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, The University of Sheffield – sequence: 5 givenname: Rob orcidid: 0000-0001-8463-1675 surname: Patro fullname: Patro, Rob email: rob.patro@cs.stonybrook.edu organization: Department of Computer Science, Stony Brook University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/30917859$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1093/bioinformatics/btw277 10.1038/nmeth.4197 10.1145/3107411.3107444 10.1371/journal.pcbi.1006361 10.1093/bioinformatics/bts635 10.1038/ni.2067 10.1101/gr.142232.112 10.1038/ncomms9885 10.1038/nmeth.4220 10.1016/j.cell.2018.02.001 10.1038/nmeth.1923 10.1186/gb-2011-12-2-r13 10.1093/bioinformatics/btx655 10.1128/mBio.00100-16 10.1002/cne.22062 10.1093/bioinformatics/btt656 10.1101/335000 10.1093/bioinformatics/btr427 10.1038/nbt.2862 10.1073/pnas.1413374111 10.1186/1471-2105-12-323 10.18632/oncotarget.15855 10.1038/nbt.3519 10.1186/s13059-016-0970-8 10.1101/gr.209601.116 10.1101/gr.176784.114 10.7554/eLife.14371 10.1016/j.cell.2015.04.044 10.1093/bioinformatics/btu288 10.1186/s13059-015-0734-x 10.1038/ncomms14049 10.1186/s13059-018-1449-6 10.1016/j.cell.2015.05.002 10.1186/s12859-019-2612-0 10.15252/embj.201798684
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Keywords	Cellular barcode UMI deduplication Quantification Single-cell RNA-seq
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References	B Li (1670_CR16) 2011; 12 H Dvinge (1670_CR33) 2014; 111 NL Bray (1670_CR27) 2016; 34 1670_CR23 J Bouquet (1670_CR34) 2016; 7 P Fratta (1670_CR38) 2018; 37 T Smith (1670_CR5) 2017; 27 A Bernáth (1670_CR30) 2011 GX Zheng (1670_CR3) 2017; 8 Y Shen (1670_CR35) 2017; 8 E Turro (1670_CR12) 2011; 12 Z Zhang (1670_CR28) 2014; 30 R Patro (1670_CR26) 2014; 32 V Svensson (1670_CR4) 2017; 14 Klein AM (1670_CR2) 2015; 161 Y Liao (1670_CR15) 2013; 30 Y Saito (1670_CR37) 2016; 5 L Zhao (1670_CR6) 2017; 34 V Ntranos (1670_CR24) 2016; 17 1670_CR42 1670_CR40 1670_CR41 Macosko EZ (1670_CR1) 2015; 161 RA Poldrack (1670_CR32) 2015; 6 1670_CR36 1670_CR39 H Sarkar (1670_CR11) 2018 X Han (1670_CR19) 2018; 172 HI Nakaya (1670_CR21) 2011; 12 C Robert (1670_CR18) 2015; 16 A Tambe (1670_CR7) 2019; 20 B Langmead (1670_CR17) 2012; 9 A Srivastava (1670_CR10) 2016; 32 R Patro (1670_CR13) 2017; 14 V Petukhov (1670_CR8) 2018; 19 GR Grant (1670_CR22) 2011; 27 A Dobin (1670_CR14) 2013; 29 CJT Ju (1670_CR29) 2017 1670_CR31 L Tian (1670_CR9) 2018; 14 F Richter (1670_CR20) 2009; 515 AM Mezlini (1670_CR25) 2013; 23
References_xml	– ident: 1670_CR31 – volume: 32 start-page: i192 issue: 12 year: 2016 ident: 1670_CR10 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw277 – volume: 14 start-page: 417 issue: 4 year: 2017 ident: 1670_CR13 publication-title: Nat Methods doi: 10.1038/nmeth.4197 – volume-title: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM-BCB ’17 year: 2017 ident: 1670_CR29 doi: 10.1145/3107411.3107444 – volume: 14 start-page: e1006361 issue: 8 year: 2018 ident: 1670_CR9 publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1006361 – volume: 29 start-page: 15 issue: 1 year: 2013 ident: 1670_CR14 publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts635 – volume: 12 start-page: 786 issue: 8 year: 2011 ident: 1670_CR21 publication-title: Nat Immunol doi: 10.1038/ni.2067 – volume: 23 start-page: 519 issue: 3 year: 2013 ident: 1670_CR25 publication-title: Genome Res doi: 10.1101/gr.142232.112 – volume: 6 start-page: 8885 year: 2015 ident: 1670_CR32 publication-title: Nat Commun doi: 10.1038/ncomms9885 – volume: 14 start-page: 381 issue: 4 year: 2017 ident: 1670_CR4 publication-title: Nat Methods doi: 10.1038/nmeth.4220 – volume: 172 start-page: 1091 issue: 5 year: 2018 ident: 1670_CR19 publication-title: Cell doi: 10.1016/j.cell.2018.02.001 – volume: 9 start-page: 357 issue: 4 year: 2012 ident: 1670_CR17 publication-title: Nat Methods doi: 10.1038/nmeth.1923 – volume: 12 start-page: R13 issue: 2 year: 2011 ident: 1670_CR12 publication-title: Genome Biol doi: 10.1186/gb-2011-12-2-r13 – volume: 34 start-page: 739 issue: 5 year: 2017 ident: 1670_CR6 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx655 – volume: 7 start-page: e00100 issue: 1 year: 2016 ident: 1670_CR34 publication-title: MBio doi: 10.1128/mBio.00100-16 – volume-title: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. BCB ’18 year: 2018 ident: 1670_CR11 – volume: 515 start-page: 538 issue: 5 year: 2009 ident: 1670_CR20 publication-title: J Comp Neurol doi: 10.1002/cne.22062 – volume: 30 start-page: 923 issue: 7 year: 2013 ident: 1670_CR15 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt656 – ident: 1670_CR40 doi: 10.1101/335000 – volume: 27 start-page: 2518 issue: 18 year: 2011 ident: 1670_CR22 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr427 – volume: 32 start-page: 462 issue: 5 year: 2014 ident: 1670_CR26 publication-title: Nat Biotechno doi: 10.1038/nbt.2862 – volume: 111 start-page: 16802 issue: 47 year: 2014 ident: 1670_CR33 publication-title: Proc Natl Acad Sci doi: 10.1073/pnas.1413374111 – ident: 1670_CR39 doi: 10.1101/335000 – volume: 12 start-page: 323 issue: 1 year: 2011 ident: 1670_CR16 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-323 – volume: 8 start-page: 27976 issue: 17 year: 2017 ident: 1670_CR35 publication-title: Oncotarget doi: 10.18632/oncotarget.15855 – volume: 34 start-page: 525 issue: 5 year: 2016 ident: 1670_CR27 publication-title: Nat Biotechnol doi: 10.1038/nbt.3519 – volume-title: Covering minimum cost arborescences year: 2011 ident: 1670_CR30 – volume: 17 start-page: 112 issue: 1 year: 2016 ident: 1670_CR24 publication-title: Genome Biol doi: 10.1186/s13059-016-0970-8 – volume: 27 start-page: 491 issue: 3 year: 2017 ident: 1670_CR5 publication-title: Genome Res doi: 10.1101/gr.209601.116 – ident: 1670_CR41 doi: 10.1101/335000 – ident: 1670_CR36 doi: 10.1101/gr.176784.114 – volume: 5 start-page: e14371 year: 2016 ident: 1670_CR37 publication-title: Elife doi: 10.7554/eLife.14371 – volume: 161 start-page: 1187 issue: 5 year: 2015 ident: 1670_CR2 publication-title: Cell doi: 10.1016/j.cell.2015.04.044 – ident: 1670_CR23 – volume: 30 start-page: i283 issue: 12 year: 2014 ident: 1670_CR28 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu288 – volume: 16 start-page: 177 issue: 1 year: 2015 ident: 1670_CR18 publication-title: Genome Biol doi: 10.1186/s13059-015-0734-x – volume: 8 start-page: 14049 year: 2017 ident: 1670_CR3 publication-title: Nat Commun doi: 10.1038/ncomms14049 – ident: 1670_CR42 – volume: 19 start-page: 78 issue: 1 year: 2018 ident: 1670_CR8 publication-title: Genome Biol doi: 10.1186/s13059-018-1449-6 – volume: 161 start-page: 1202 issue: 5 year: 2015 ident: 1670_CR1 publication-title: Cell doi: 10.1016/j.cell.2015.05.002 – volume: 20 start-page: 32 issue: 1 year: 2019 ident: 1670_CR7 publication-title: BMC Bioinformatics doi: 10.1186/s12859-019-2612-0 – volume: 37 start-page: e98684 issue: 11 year: 2018 ident: 1670_CR38 publication-title: EMBO J doi: 10.15252/embj.201798684
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Snippet	We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping,... Abstract We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read...
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SubjectTerms	Algorithms Animal Genetics and Genomics Animals Bioinformatics Biomedical and Life Sciences Cellular barcode Datasets DNA Barcoding, Taxonomic Evolutionary Biology Gene expression Gene mapping genes Genomes Genomics Human Genetics Humans Life Sciences Method Mice Microbial Genetics and Genomics nucleotide sequences pipelines Plant Genetics and Genomics Quantification Ribonucleic acid RNA sequence analysis Sequence Analysis, RNA Single-Cell Analysis Single-cell RNA-seq Software Transcription UMI deduplication
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Title	Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
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