Evidence map›Paper›PMID 37425881›Full record

ArticlebioRxiv : the preprint server for biology2023

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Byung June Ko, Alex Ostrovsky, Marc Palmada-Flores, Brandon D Pickett, Keon Rabbani and 27 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

37 authors.

Delphine LarivièreDept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA.
Linelle AbuegVertebrate Genome Laboratory, The Rockefeller University, USA.
Nadolina BrajukaVertebrate Genome Laboratory, The Rockefeller University, USA.
Cristóbal Gallardo-AlbaBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Bjorn GrüningBioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
Byung June KoDepartment of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Alex OstrovskyDepartments of Biology and Computer Science, Johns Hopkins University, USA.
Marc Palmada-FloresDepartment of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.
Brandon D PickettGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Keon RabbaniDepartment of Quantitative and Computational Biology, University of Southern California.
Jennifer R BalaccoVertebrate Genome Laboratory, The Rockefeller University, USA.
Mark ChaissonDepartment of Quantitative and Computational Biology, University of Southern California.
Haoyu ChengDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Joanna CollinsWellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom.
Alexandra DenisovaFaculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
Olivier FedrigoVertebrate Genome Laboratory, The Rockefeller University, USA.
Guido Roberto GalloDepartment of Biosciences, University of Milan, Milan, Italy.
Alice Maria GianiBMRI, Weill Cornell Medical College, New York, 10021, USA.
Grenville MacDonald GooderVertebrate Genome Laboratory, The Rockefeller University, USA.
Nivesh JainVertebrate Genome Laboratory, The Rockefeller University, USA.
Cassidy JohnsonVertebrate Genome Laboratory, The Rockefeller University, USA.
Heebal KimDepartment of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Chul LeeInterdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
Tomas Marques-BonetDepartment of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.
Brian O'TooleVertebrate Genome Laboratory, The Rockefeller University, USA.
Arang RhieGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Simona SecomandiDepartment of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
Marcella SozzoniUniversity of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI).
Tatiana TilleyVertebrate Genome Laboratory, The Rockefeller University, USA.
Marcela Uliano-SilvaTree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom.
Marius van den BeekDept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA.
Robert M WaterhouseDepartment of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
Adam M PhillippyGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Erich D JarvisVertebrate Genome Laboratory, The Rockefeller University, USA.
Michael C SchatzDepartments of Biology and Computer Science, Johns Hopkins University, USA.
Anton NekrutenkoDept. of Biochemistry and Molecular Biology, Pennsylvania State University, USA.
Giulio FormentiVertebrate Genome Laboratory, The Rockefeller University, USA.

Funding

Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8M
Democratization of Data Analysis in Life Sciences Through GalaxyU41HG006620 · NHGRI · PENNSYLVANIA STATE UNIVERSITY, THE · PI NEKRUTENKO, ANTON, SCHATZ, MICHAEL · 2012 to 2020
$14.4M
A Federated Galaxy for user-friendly large-scale cancer genomics researchU24CA231877 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI GOECKS, JEREMY · 2018 to 2022
$3.9M
Integrative genomic and epigenomic analysis of cancer using long read sequencingU01CA253481 · NCI · JOHNS HOPKINS UNIVERSITY · PI SCHATZ, MICHAEL · 2021 to 2023
$1.1M
NCI NIH HHS U01 CA253481NCI NIH HHS U24 CA231877NHGRI NIH HHS U24 HG010263NHGRI NIH HHS U41 HG006620
6 · The paper itself

Abstract

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

Indexed as

accessibleGenome assemblylarge genomesmodularityopensourcepublicreproducibilityscalable

Identifiers

PMID37425881
PMCPMC10327048

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.