Evidence map›Paper›PMID 32183840›Full record

ArticleGenome biology2020

Benchmarking of computational error-correction methods for next-generation sequencing data.

Keith Mitchell, Jaqueline J Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman and 16 more

Abstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

25 citing papers in PubMed.

  1. Review
  2. Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026
    Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Keith MitchellDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Jaqueline J BritoDepartment of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
Igor MandricDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Qiaozhen WuDepartment of Mathematics, University of California Los Angeles, 520 Portola Plaza, Los Angeles, CA, 90095, USA.
Sergey KnyazevDepartment of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA.
Sei ChangDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Lana S MartinDepartment of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
Aaron KarlsbergDepartment of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
Ekaterina GerasimovDepartment of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA.
Russell LittmanUCLA Bioinformatics, 621 Charles E Young Dr S, Los Angeles, CA, 90024, USA.
Brian L HillDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Nicholas C WuDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Harry Taegyun YangDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Kevin HsiehDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Linus ChenDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Eli LittmanDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Taylor ShabaniDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
German EnikDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Douglas YaoDepartment of Molecular, Cell, and Developmental Biology, University of California Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
Ren SunDepartment of Molecular and Medical Pharmacology, University of California Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
Jan SchroederEpigenetics & Reprogramming Laboratory, Monash University, 15 Innovation Walk, Melbourne, VIC, 3800, Australia.
Eleazar EskinDepartment of Computer Science, University of California Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
Alex ZelikovskyDepartment of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA.
Pavel SkumsDepartment of Computer Science, Georgia State University, 1 Park Place, Atlanta, GA, 30303, USA.
Mihai PopDepartment of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.
Serghei MangulDepartment of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA. serghei.mangul@gmail.com.

Funding

Developing a Pathway from Genetic Locus to Gene for Complex Traits in RodentsR01MH115979 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FLINT, JONATHAN · 2018 to 2022
$3.5M
Genetic pathways for impulsivity and drug reinforcement: DNA and transcriptome variation in miceU01DA041602 · NIDA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ESKIN, ELEAZAR, JENTSCH, J. DAVID · 2017 to 2021
$3.2M
QUBBD: VIRAL EVOLUTION AND SPREAD OF INFECTIOUS DISEASE IN COMPLEX NETWORK: BIG DATA ANALYSIS AND MODELINGR01EB025022 · NIBIB · GEORGIA STATE UNIVERSITY · PI SKUMS, PAVEL, VANNBERG, FREDRIK · 2017 to 2019
$891k
Undergraduate Research Experience in Neuropsychiatric GenomicsR25MH109172 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ESKIN, ELEAZAR, FREIMER, NELSON B. · 2016 to 2020
$429k
Mechanistic understanding of influenza-host interactions from a zoonotic perspectiveK99AI139445 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI WU, NICHOLAS C. · 2019 to 2020
$132k
NIAID NIH HHS K99 AI139445NIBIB NIH HHS R01 EB025022NIDA NIH HHS U01 DA041602NIMH NIH HHS R01 MH115979NIMH NIH HHS R25 MH109172
6 · The paper itself

Abstract

backgroundRecent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown.

resultsIn this paper, we evaluate the ability of error correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error-correction methods.

conclusionsIn terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity.

Indexed as

AlgorithmsHigh-Throughput Nucleotide SequencingBenchmarkingComputational BiologyHumansReceptors, Antigen, T-CellVirusesWhole Genome SequencingReceptors, Antigen, T-Cell

Identifiers

PMID32183840
PMCPMC7079412

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.