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Trans-NanoSim characterizes and simulates nanopore RNA-seq data

View ORCID ProfileSaber Hafezqorani, Chen Yang, View ORCID ProfileKa Ming Nip, View ORCID ProfileRené L Warren, View ORCID ProfileInanc Birol
doi: https://doi.org/10.1101/800110
Saber Hafezqorani
1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
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  • ORCID record for Saber Hafezqorani
Chen Yang
1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
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Ka Ming Nip
1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
2Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
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René L Warren
1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
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  • ORCID record for René L Warren
Inanc Birol
1Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
3Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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  • For correspondence: ibirol@bcgsc.ca
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Abstract

We introduce Trans-NanoSim, the first tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data. Through benchmarking on sets of nanopore reads from human and mouse reference transcriptomes, we show the robustness of Trans-NanoSim in capturing the characteristics of nanopore cDNA and direct RNA reads. As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim would facilitate the rapid development of analytical tools for nanopore RNA-seq data. Trans-NanoSim is freely accessible at https://github.com/bcgsc/NanoSim

Footnotes

  • shafezqorani{at}bcgsc.ca, cheny{at}bcgsc.ca, kmnip{at}bcgsc.ca, rwarren{at}bcgsc.ca

  • https://github.com/bcgsc/NanoSim

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-ND 4.0 International license.
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Posted October 10, 2019.
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Trans-NanoSim characterizes and simulates nanopore RNA-seq data
Saber Hafezqorani, Chen Yang, Ka Ming Nip, René L Warren, Inanc Birol
bioRxiv 800110; doi: https://doi.org/10.1101/800110
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Trans-NanoSim characterizes and simulates nanopore RNA-seq data
Saber Hafezqorani, Chen Yang, Ka Ming Nip, René L Warren, Inanc Birol
bioRxiv 800110; doi: https://doi.org/10.1101/800110

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