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SMART2: Multi-library Statistical Mitogenome Assembly with Repeats

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Book cover Computational Advances in Bio and Medical Sciences (ICCABS 2019)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12029))

Abstract

SMART2 is an enhanced version of the SMART pipeline for mitogenome assembly from low-coverage whole-genome sequencing (WGS) data. Novel features include automatic selection of the optimal number of read pairs used for assembly and the ability to assemble multiple sequencing libraries when available. SMART2 succeeded in generating mitochondrial sequences for 26 metazoan species with WGS data but no previously published mitogenomes in NCBI databases. The SMART2 pipeline is publicly available via a user-friendly Galaxy interface at https://neo.engr.uconn.edu/?tool_id=SMART2.

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Author information

Authors and Affiliations

  1. Computer Science and Engineering Department, University of Connecticut, Storrs, Mansfield, CT, USA

    Fahad Alqahtani & Ion Măndoiu

  2. National Center for Artificial Intelligence and Big Data Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia

    Fahad Alqahtani

Authors
  1. Fahad Alqahtani
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  2. Ion Măndoiu
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Corresponding author

Correspondence to Ion Măndoiu .

Editor information

Editors and Affiliations

  1. University of Connecticut, Storrs, CT, USA

    Ion Măndoiu

  2. Virginia Tech, Blacksburg, VA, USA

    T. M. Murali

  3. Florida International University, Miami, FL, USA

    Giri Narasimhan

  4. University of Connecticut, Storrs, CT, USA

    Sanguthevar Rajasekaran

  5. Georgia State University, Atlanta, GA, USA

    Pavel Skums

  6. Georgia State University, Atlanta, GA, USA

    Alexander Zelikovsky

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Alqahtani, F., Măndoiu, I. (2020). SMART2: Multi-library Statistical Mitogenome Assembly with Repeats. In: Măndoiu, I., Murali, T., Narasimhan, G., Rajasekaran, S., Skums, P., Zelikovsky, A. (eds) Computational Advances in Bio and Medical Sciences. ICCABS 2019. Lecture Notes in Computer Science(), vol 12029. Springer, Cham. https://doi.org/10.1007/978-3-030-46165-2_15

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  • DOI: https://doi.org/10.1007/978-3-030-46165-2_15

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-46164-5

  • Online ISBN: 978-3-030-46165-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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