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RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

Ivan de la Rubia, View ORCID ProfileAkanksha Srivastava, Wenjing Xue, Joel A Indi, Silvia Carbonell-Sala, View ORCID ProfileJulien Lagarde, View ORCID ProfileM Mar Albà, View ORCID ProfileEduardo Eyras
doi: https://doi.org/10.1101/2020.02.08.939942
Ivan de la Rubia
1EMBL Australia Partner Laboratory Network at the Australian National University, Acton ACT 2601, Canberra, Australia
2Pompeu Fabra University (UPF), E08003 Barcelona, Spain
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Akanksha Srivastava
1EMBL Australia Partner Laboratory Network at the Australian National University, Acton ACT 2601, Canberra, Australia
3Australian National University, Acton ACT 2601, Canberra, Australia
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  • ORCID record for Akanksha Srivastava
Wenjing Xue
1EMBL Australia Partner Laboratory Network at the Australian National University, Acton ACT 2601, Canberra, Australia
3Australian National University, Acton ACT 2601, Canberra, Australia
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Joel A Indi
1EMBL Australia Partner Laboratory Network at the Australian National University, Acton ACT 2601, Canberra, Australia
4Universidade de Lisboa, Lisboa, Portugal
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Silvia Carbonell-Sala
2Pompeu Fabra University (UPF), E08003 Barcelona, Spain
5Centre for Regulatory Genomics (CRG), E08001 Barcelona, Spain
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Julien Lagarde
2Pompeu Fabra University (UPF), E08003 Barcelona, Spain
5Centre for Regulatory Genomics (CRG), E08001 Barcelona, Spain
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  • ORCID record for Julien Lagarde
M Mar Albà
2Pompeu Fabra University (UPF), E08003 Barcelona, Spain
6Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
7Hospital del Mar Medical Research Institute (IMIM), E08001 Barcelona, Spain
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  • For correspondence: malba@imim.es eduardo.eyras@anu.edu.au
Eduardo Eyras
1EMBL Australia Partner Laboratory Network at the Australian National University, Acton ACT 2601, Canberra, Australia
3Australian National University, Acton ACT 2601, Canberra, Australia
6Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
7Hospital del Mar Medical Research Institute (IMIM), E08001 Barcelona, Spain
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  • ORCID record for Eduardo Eyras
  • For correspondence: malba@imim.es eduardo.eyras@anu.edu.au
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Abstract

Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes from any sample. However, current methods for transcript identification and quantification rely of mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. Here we present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts. RATTLE provides unprecedented access to transcriptomes from any sample and species without relying on a reference or additional technologies.

Competing Interest Statement

E.E. has received support from Oxford Nanopore Technologies (ONT) to present the results from this manuscript at scientific conferences. However, ONT played no role in the algorithm or software developments, study design, analysis, or preparation of the manuscript.

Footnotes

  • We have performed additional benchmarking analyses and have clarified some of the algorithmic details.

  • https://github.com/comprna/RATTLE

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 08, 2022.
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RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, Joel A Indi, Silvia Carbonell-Sala, Julien Lagarde, M Mar Albà, Eduardo Eyras
bioRxiv 2020.02.08.939942; doi: https://doi.org/10.1101/2020.02.08.939942
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RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, Joel A Indi, Silvia Carbonell-Sala, Julien Lagarde, M Mar Albà, Eduardo Eyras
bioRxiv 2020.02.08.939942; doi: https://doi.org/10.1101/2020.02.08.939942

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