Evidence map›Paper›PMID 39282325›Full record

ArticlebioRxiv : the preprint server for biology2025

Metapipeline-DNA: A Comprehensive Germline & 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 34 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

44 authors.

Yash PatelDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-3113-7010
Chenghao ZhuDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-1674-4533
Takafumi N YamaguchiDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-1082-3871
Nicholas K WangDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-1043-3072
Nicholas WiltsieDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0009-0000-7683-5299
Nicole ZeltserDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-7246-2771
Alfredo E GonzalezDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-8963-3135
Helena K WinataDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-1001-5316
Yu PanDepartment of Human Genetics, University of California, Los Angeles, USA.
Mohammed Faizal Eeman MootorDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-4154-455X
Timothy SandersDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-5596-323X
Sorel T Fitz-GibbonDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-7090-5719
Cyriac KandothDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-1345-3573
Julie LivingstoneDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-8424-3768
Lydia Y LiuDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-6026-3169
Benjamin CarlinDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-9360-9143
Aaron HolmesDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-1012-7879
Jieun OhDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-8961-8645
John SahrmannDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-6000-0908
Shu TaoDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-5177-6771
Stefan EngDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-5245-6507
Rupert Hugh-WhiteDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-3351-8925
Kiarod PashminehazarDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0009-0007-4824-8733
Andrew ParkDepartment of Human Genetics, University of California, Los Angeles, USA.
Arpi BeshlikyanDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-0700-4827
Madison JordanDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-4952-373X
Selina WuDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-5206-0150
Mao TianDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-4418-5153
Jaron ArbetDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-4218-2458
Beth NeilsenDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-4859-6486
Roni HaasDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-1505-2965
Yuan Zhe BughDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-3662-3475
Gina KimDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-9265-5490
Joseph SalmingoDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0009-0003-4948-9505
Wenshu ZhangDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0009-0005-1357-3531
Aakarsh AnandDepartment of Human Genetics, University of California, Los Angeles, USA.
Edward HwangDepartment of Human Genetics, University of California, Los Angeles, USA.
Anna Neiman-GoldenDepartment of Human Genetics, University of California, Los Angeles, USA.
Philippa SteinbergDepartment of Human Genetics, University of California, Los Angeles, USA.
Wenyan ZhaoDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-9647-8006
Prateek AnandDepartment of Human Genetics, University of California, Los Angeles, USA.
Raag AgrawalDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0001-8222-3117
Brandon L TsaiDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0002-7372-3504
Paul C BoutrosDepartment of Human Genetics, University of California, Los Angeles, USA.ORCID 0000-0003-0553-7520

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5M
UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
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
UCLA-Caltech Medical Scientist Training ProgramT32GM152342 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Olujimi A Ajijola, David Wayne Dawson · 2024 to 2026
$5.3M
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
Randomized Trial of Exercise Therapy on Markers of Progression in Localized Prostate Cancer:R01CA272678 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI Paul Christopher Boutros, LEE W JONES · 2022 to 2026
$3.6M
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
NCI NIH HHS F31 CA281168NCI NIH HHS P30 CA016042NCI NIH HHS R01 CA244729NCI NIH HHS R01 CA268380NCI NIH HHS R01 CA270108NCI NIH HHS R01 CA272678NCI NIH HHS T32 CA009056NCI NIH HHS U24 CA248265NCI NIH HHS U2C CA271894NHGRI NIH HHS T32 HG002536NHGRI NIH HHS U54 HG012517NIGMS NIH HHS T32 GM008042NIGMS NIH HHS T32 GM152342NLM NIH HHS T15 LM013976
6 · The paper itself

Abstract

The price, quality and throughout 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 meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data-visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust 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.

Identifiers

PMID39282325
PMCPMC11398472

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.