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An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development

Gunjan Baid, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Howard Yang, Pi-Chuan Chang, View ORCID ProfileAndrew Carroll
doi: https://doi.org/10.1101/2020.12.11.422022
Gunjan Baid
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Maria Nattestad
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Alexey Kolesnikov
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Sidharth Goel
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Howard Yang
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Pi-Chuan Chang
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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Andrew Carroll
1Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
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  • ORCID record for Andrew Carroll
  • For correspondence: awcarroll@google.com
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Abstract

Accurate standards and extensive development datasets are the foundation of technical progress. To facilitate benchmarking and development, we sequence 9 samples, covering the Genome in a Bottle truth sets on multiple instruments (NovaSeq, HiSeqX, HiSeq4000, PacBio Sequel II System) and sample preparations (PCR-Free, PCR-Positive) for both whole genome and multiple exome kits. We benchmark pipelines, quantifying strengths and limitations for sequencing and analysis methods. We identify variability within and between instruments, preparation methods, and analytical pipelines, across various sequencing depths. We discuss the relevance of this variability to downstream analyses, and strategies to reduce variability.

Competing Interest Statement

All authors are employees of Google LLC and own Alphabet stock as part of the standard compensation package. This study was funded by Google LLC.

Footnotes

  • https://console.cloud.google.com/storage/browser/brain-genomics-public/research/sequencing/

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 4.0 International license.
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Posted December 11, 2020.
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An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development
Gunjan Baid, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Howard Yang, Pi-Chuan Chang, Andrew Carroll
bioRxiv 2020.12.11.422022; doi: https://doi.org/10.1101/2020.12.11.422022
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An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development
Gunjan Baid, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Howard Yang, Pi-Chuan Chang, Andrew Carroll
bioRxiv 2020.12.11.422022; doi: https://doi.org/10.1101/2020.12.11.422022

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