Evidence map›Paper›PMID 41850291›Full record

ArticleCell reports methods2026

Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.

Yash Patel, Chenghao Zhu, Takafumi N Yamaguchi, Nicholas K Wang, Nicholas Wiltsie, Nicole Zeltser, Alfredo E Gonzalez, Helena K Winata, Yu Pan, Mohammed Faizal Eeman Mootor and 33 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Identification of non-canonical peptides with moPepGen.bioRxiv : the preprint server for biology · 2025
    Article
  4. Article
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

43 authors.

Yash PatelDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Chenghao ZhuDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Takafumi N YamaguchiDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Nicholas K WangDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Nicholas WiltsieDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Nicole ZeltserDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
Alfredo E GonzalezDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Helena K WinataDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Yu PanDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Mohammed Faizal Eeman MootorDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Timothy SandersDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Sorel T Fitz-GibbonDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Cyriac KandothDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Julie LivingstoneDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
Lydia Y LiuDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
Benjamin CarlinDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Aaron HolmesDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Jieun OhDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
John SahrmannDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Shu TaoDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
Stefan EngDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Rupert Hugh-WhiteDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Kiarod PashminehazarDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Arpi BeshlikyanDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Madison JordanDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Selina WuDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Mao TianDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Jaron ArbetDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Beth NeilsenDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Roni HaasDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Yuan Zhe BughDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Gina KimDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Joseph SalmingoDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Wenshu ZhangDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Aakarsh AnandDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Edward HwangDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Anna Neiman-GoldenDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Philippa SteinbergDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Wenyan ZhaoDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
Prateek AnandDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Raag AgrawalDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
Brandon L TsaiDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
Paul C BoutrosDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA; Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA. Electronic address: pboutros@sbpdiscovery.org.

Funding

Tool Core- BoutrosU54HG012517 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BUI, ALEX, PING, PEIPEI · 2022 to 2025
$10.6M
TUMOR CELL SURFACES AND CHROMOSOMEST32CA009056 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Gay M Crooks, David A. Nathanson · 1985 to 2026
$10.5M
Training Grant in Genomic Analysis and InterpretationT32HG002536 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Valerie A Arboleda, Harold Pimentel · 2002 to 2026
$8.6M
Advancing method benchmarking and data sharing through crowd-sourced competitions in cancer researchU24CA248265 · NCI · SAGE BIONETWORKS · PI BOUTROS, PAUL CHRISTOPHER, VARMA, SUSHEEL · 2020 to 2024
$4.1M
The Evolution of Sarcoma Drug Sensitivity through Time and SpaceR01CA244729 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BOUTROS, PAUL CHRISTOPHER, SORAGNI, ALICE · 2020 to 2024
$3.4M
Virginia-UCLA-Toronto Biomarker Characterization CenterU2CCA271894 · NCI · OLD DOMINION UNIVERSITY · PI Paul Christopher Boutros, OLIVER John SEMMES · 2022 to 2026
$3.2M
Germline Determinants of Prostate Cancer EvolutionR01CA270108 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PAUL T. SPELLMAN · 2023 to 2026
$2.9M
Statistical methods for genomic analysis of heterogeneous tumorsR01CA268380 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Wenyi Wang · 2022 to 2026
$2.4M
Predicting prostate cancer clinical outcomes with germline genomic biomarkersF31CA281168 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZELTSER, NICOLE · 2024 to 2025
$83k
NCI NIH HHS F31 CA281168NCI NIH HHS R01 CA244729NCI NIH HHS R01 CA268380NCI NIH HHS R01 CA270108NCI NIH HHS T32 CA009056NCI NIH HHS U24 CA248265NCI NIH HHS U2C CA271894NHGRI NIH HHS T32 HG002536NHGRI NIH HHS U54 HG012517
6 · The paper itself

Abstract

The price, quality, and throughput of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial, and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow metapipeline called metapipeline-DNA. It analyzes targeted and whole-genome sequencing data from raw reads through preprocessing, feature detection by multiple algorithms, quality control, and data-visualization. Each step can be run independently and is supported by robust software engineering including automated failure-recovery, granular testing, and consistent verifications of inputs, outputs, and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data, and is open-source under the GPLv2 license.

Indexed as

GenomicsGerm CellsHigh-Throughput Nucleotide SequencingSequence Analysis, DNASoftwareAlgorithmsHumansCP: computational biologyCP: geneticsDNA sequencinggenomicsnext-generation sequencingsubclonal reconstructionvariant calling

Identifiers

PMID41850291
PMCPMC13030954

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.