Paper · 20644199

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A and 10 others. Genome Res, 2010. Cited by 21,231 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Papers, record 20644199. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/20644199

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.; PubMed
Journal: Genome Res; PubMed
Year: 2010; PubMed
Publication types: Journal Article, Research Support, N.I.H., Extramural; PubMed
PubMed: https://pubmed.ncbi.nlm.nih.gov/20644199/; PubMed
DOI: https://doi.org/10.1101/gr.107524.110; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC2928508/; PubMed
The journal: https://conductscience.org/library/journal-index/9518021; PubMed
Citations, by iCite: 21,231; iCite
Relative citation ratio, by iCite: 559; iCite
Revised in PubMed: 2026-07-09; PubMed

Authors11

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

Order	Author	Forename
1	McKenna A	Aaron
2	Hanna M	Matthew
3	Banks E	Eric
4	Sivachenko A	Andrey
5	Cibulskis K	Kristian
6	Kernytsky A	Andrew
7	Garimella K	Kiran
8	Altshuler D	David
9	Gabriel S	Stacey
10	Daly M	Mark

1 to 10 of 11Source PubMed

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Topics5

NLM's MeSH indexing of the paper, its major topics first.

MeSH term	Major
Genome	Major topic
Genomics	Major topic
Sequence Analysis, DNA	Major topic
Software	Major topic
Base Sequence

Source PubMed

Grants4

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes it	Agency	Country	NIH project	Stated by	Source
P30 DK043351	NIDDK NIH HHS	United States	P30DK043351	PubMed and NIH	NIH RePORTER
U01 HG005208	NHGRI NIH HHS	United States	U01HG005208	PubMed and NIH	NIH RePORTER
U54 HG003067	NHGRI NIH HHS	United States	U54HG003067	PubMed and NIH	NIH RePORTER
54 HG003067	NHGRI NIH HHS	United States		PubMed	PubMed

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References25

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

Order	PMID	Title	Journal	Year	In Papers	Source
1	11,591,649	SSAHA: a fast search method for large DNA databases.	Genome Res	2001	https://conductscience.org/library/papers/11591649	PubMed
2	18,421,352	The complete genome of an individual by massively parallel DNA sequencing.	Nature	2008	https://conductscience.org/library/papers/18421352	PubMed
3	11,125,122	dbSNP: the NCBI database of genetic variation.	Nucleic Acids Res	2001	https://conductscience.org/library/papers/11125122	PubMed
4	18,227,114	SOAP: short oligonucleotide alignment program.	Bioinformatics	2008	https://conductscience.org/library/papers/18227114	PubMed
5	19,654,119	ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.	Bioinformatics	2009	https://conductscience.org/library/papers/19654119	PubMed
6	16,056,220	Genome sequencing in microfabricated high-density picolitre reactors.	Nature	2005	https://conductscience.org/library/papers/16056220	PubMed
7	18,714,091	Mapping short DNA sequencing reads and calling variants using mapping quality scores.	Genome Res	2008	https://conductscience.org/library/papers/18714091	PubMed
8	19,844,228	Computation for ChIP-seq and RNA-seq studies.	Nat Methods	2009	https://conductscience.org/library/papers/19844228	PubMed
9	19,505,943	The Sequence Alignment/Map format and SAMtools.	Bioinformatics	2009	https://conductscience.org/library/papers/19505943	PubMed
10	14,685,227	The International HapMap Project.	Nature	2003	https://conductscience.org/library/papers/14685227	PubMed

1 to 10 of 25

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Cited by16,782

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 21,231 citations.

PMID	Title	Journal	Year	In Papers	Source
42,989,007	Claudin-1 as a potential marker of stress-induced premature senescence in vascular smooth muscle cells.	Geroscience	2026	https://conductscience.org/library/papers/42989007	PubMed
42,988,903	Nondisruptive 3D profiling of combinations of epigenetic marks in single cells.	Nat Methods	2026	https://conductscience.org/library/papers/42988903	PubMed
42,985,618	Promises and limitations of current ancient human epigenetic clocks.	iScience	2026	https://conductscience.org/library/papers/42985618	PubMed
42,984,849	Biogeography of Argentine Stem Weevil Invasion of Southern New Zealand and Two Offshore Islands.	Ecol Evol	2026	https://conductscience.org/library/papers/42984849	PubMed
42,983,097	In vivo CAR-T double knockout screen maps synergistic antitumour gene pairs.	Nature	2026	https://conductscience.org/library/papers/42983097	PubMed
42,981,403	Independent origin of genomic imprinting in placental fish.	Sci Adv	2026	https://conductscience.org/library/papers/42981403	PubMed
42,980,837	Genome-wide SNP analysis identifies population structure and genetic differentiation in Anopheles stephensi.	Parasitol Res	2026	https://conductscience.org/library/papers/42980837	PubMed
42,979,777	Telomere-to-telomere genome assembly of the endangered Jacktree (Sinojackia xylocarpa Hu) reveals its centromeric landscape and evolutionary dilemma as a small population.	Plant J	2026	https://conductscience.org/library/papers/42979777	PubMed
42,976,958	Genomic mechanisms underlying Bombay duck's rapid population surge.	Proc Biol Sci	2026	https://conductscience.org/library/papers/42976958	PubMed
42,972,604	Exome analysis of Indian ulcerative colitis reveals novel genes affecting epithelial integrity, DNA repair, trafficking, and immune signalling.	Hum Genomics	2026	https://conductscience.org/library/papers/42972604	PubMed

1 to 10 of 16,782

See all 16,782 cited by

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed: 2026-11-06; PubMed
iCite: 2026-11-05; iCite
PMC's ID file: 2026-11-05; PMC's ID file
NIH RePORTER's grant and paper links: 2026-11-01; NIH RePORTER's grant and paper links
Trials: 2026-11-12
Gene search: 2026-11-11
Pipelines: 2026-09-18

Sources 11

ChEMBL, through Open TargetsCC BY-SA 3.0
ClinicalTrials.govNo license stated
HGNCCC0
iCiteCC BY 4.0
NCBI GenePublic domain (US government)
NIH RePORTER's grant and paper linksPublic domain
Open TargetsCC0 1.0
PMC's ID filePublic domain (US government)
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0

Each source's terms

ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
ClinicalTrials.govnone stated
HGNCCC0: https://www.genenames.org/about/license/
iCiteCC BY 4.0
NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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