The Genome Analysis Toolkit
A MapReduce framework for analyzing next-generation DNA sequencing data
Bibliographic Data
| ID | 23357374 |
|---|---|
| Authors | Aaron McKenna (0000-0001-8277-6512, Broad Institute), Matthew G Hanna (0000-0002-7536-1746, Broad Institute), Matthew Hanna, Eric Banks (0000-0001-9615-2372, Broad Institute), Andrey Sivachenko (Broad Institute), Kristian Cibulskis (0000-0003-1343-1582, Broad Institute), Andrew Kernytsky (Broad Institute), Kiran Garimella (0000-0002-6212-5736, Broad Institute), David Altshuler (0000-0002-7250-4107, Broad Institute), Stacey Gabriel (0000-0001-6939-2215, Broad Institute), Mark Daly, Mark J Daly (0000-0002-0949-8752, Broad Institute), Mark A DePristo (0000-0001-9928-045X, Broad Institute) |
| Year | 2010 |
| Volume | 20 |
| Issue | 9 |
| Pages | 1297-1303 |
| Publication date | 2010-09-01 |
| Peer Reviewed | Yes |
| Open Access | No |
| Type | ARTICLE |
| Venue | Genome Research (JOURNAL) |
| Journal identifiers | ISSN: 1088-9051 • E-ISSN: 1549-5469 |
| Publisher | Cold Spring Harbor Laboratory (PUBLISHER) |
| DOI | 10.1101/gr.107524.110 |
| PMID | 20644199 |
| PMCID | PMC2928508 |
| OpenAlex | W2119180969 |
| Language | EN |
| Citations received | 76 |
| References cited | 26 |
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
1000 Genomes Project · Biology · Computational biology · Correctness · DNA · DNA sequencing · Genome · Programming language · Set (abstract data type) · Single-nucleotide polymorphism · Algorithms and Data Compression · Computer Science · Gene expression and cancer classification · Genetics · Genomics and Phylogenetic Studies
Ancient mitochondrial genomes of Erlitou dogs reveal diverse population dynamics during early state formation in China
Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates
Paleogenetic Analysis of the Residents from the Moscow Kremlin’s Podol (Lower Area) of the 14th Century (According to the Materials of Excavations in the Taynitsky Garden)
Identification of a Rare PSEN1 Mutation (Thr119Ile) in Late-Onset Alzheimer’s Disease With Early Presentation of Behavioral Disturbance
Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes
Population genomics of Bronze Age Eurasia
MapDamage2.0
Genome flux and stasis in a five millennium transect of European prehistory
The Simons Genome Diversity Project
The prehistoric peopling of Southeast Asia
Angsd
Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
Ancient gene flow from early modern humans into Eastern Neanderthals
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
Genetic evidence for two founding populations of the Americas
Ancient human genomes suggest three ancestral populations for present-day Europeans
Second-generation PLINK
Ancient genomes indicate population replacement in Early Neolithic Britain
Eager
Fast gapped-read alignment with Bowtie 2
Genomic and archaeological evidence suggest a dual origin of domestic dogs
Indigenous Ancestry and Admixture in the Uruguayan Population
Dendritic Spine in Autism Genetics
Expanding the Phenotypic Spectrum of Ecel1-Associated Distal Arthrogryposis
Optimal Protocols and Management of Clinical and Genomic Data Collection to Assist in the Early Diagnosis and Treatment of Multiple Congenital Anomalies
A Novel Lins1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability
Primary Adrenal Insufficiency, Complete Sex Reversal, and Unique Clinical Phenotype in a Patient with Severe CYP11A1 (P450scc) Deficiency—Case Report and Literature Overview
Genetic architecture and clinical features of Tourette syndrome in a child and adolescent cohort
Novel missense variants in brain morphogenic genes associated with depression and schizophrenia
The Pattern for Preachers
Identification of a Novel FAM83H Mutation and Management of Hypocalcified Amelogenesis Imperfecta in Early Childhood
Genome-wide SNPs reveal novel patterns of spatial genetic structure in Aedes albopictus (Diptera Culicidae) population in China
Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii
Middle Helladic Tombs at Nydri Plain, Lefkas Island. An Archaeological and Paleoanthropological Study
RNA-seq transcriptome and pathway analysis of the medicinal mushroom Lignosus tigris (Polyporaceae) offer insights into its bioactive compounds with anticancer and antioxidant potential
Ancient DNA study of Cervus canadensis unearthed from the Royal Sacrificial Site of the Northern Wei Dynasty in Inner Mongolia Autonomous Region, China
Ancient dog DNA reveals the human livelihood mode transitions during the late Neolithic in Northeastern China
Ancient cattle DNA provides novel insight into the subsistence mode transition from the late Neolithic to Bronze Age in the Nenjiang River Basin
Ancient genomes reveal a rare maternal lineage of domestic horse in China
The secrets of Sobek – A crocodile mummy mitogenome from ancient Egypt
Horse males became over-represented in archaeological assemblages during the Bronze Age
Complete mitogenomes of ancient Caribbean Guinea pigs (Cavia porcellus)
The kinship of two 12th Dynasty mummies revealed by ancient DNA sequencing
Ancient genomic evidence of genetic integration among Xianbei populations in the Central Plains of China
A population history of Tokelau – genetic variation and change in atoll populations
Correlation analysis of genetic admixture and social identification with body mass index in a Native American Community
Demographic history of the Jomon people
Ancient DNA refines taxonomic classification of Roman equids north of the Alps, elaborated with osteomorphology and geometric morphometrics
Ancient Mycobacterium leprae genomes from the mediaeval sites of Chichester and Raunds in England
Ancient DNA reveals the origin and history of early dogs in northeastern China
The limits and potential of paleogenomic techniques for reconstructing grapevine domestication
Ancient mitochondrial genome reveals matrilineal genetic inheritance of Chinese goats
The genetic landscape of Mediterranean North African populations through complete mtDNA sequences
Ancient sacrificial dog DNA reveals North–South interactions during the late Shang Dynasty in northern China
Utilization of wild animal resources on the silk road
Genetic structure of Shandong taurine cattle in Han Dynasty
Genetic variation of olfactory receptor gene family in a Japanese population
The history of ancient Japanese dogs revealed by mitogenomes
Male-driven admixture facilitated subsistence shift in northern China
Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi
Genomic epidemiology of Sars-CoV-2 during the first four waves in Mozambique
Ancient goat DNA reveals East–West cultural interaction across Eurasia
Ancient DNA provides new insights into the history of Xinjiang domestic horses
Genetic Diversity, Genetic Structure, and Demographic History of Black Snub‐Nosed Monkey ( Rhinopithecus strykeri ) in the Gaoligong Mountains, Southwestern China
Weak effects of common genetic variation in oxytocin and vasopressin receptor genes on rhesus macaque social behavior
Transcriptomic-proteomics-anticoagulant bioactivity integrated study of Pheretima guillemi
Gelada (Theropithecus gelada) genomic diversity sheds light on the biogeography of an endemic species of the Ethiopian highlands
The Promise and Practicality of Population Genomics Research with Endangered Species
The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population
Elevated diversity in loci linked to facial morphology is consistent with the hypothesis that individual facial recognition is important across hominoids
Ancient DNA sheds light on the mating strategies and genetic identity of Han nobles during the Northern and Southern Dynasties
Life beyond big data
Mitogenomics of the Extinct Cave Lion, Panthera spelaea (Goldfuss, 1810), Resolve its Position within the Panthera Cats
Molecular archaeological study of horse remains unearthed from Jiulongshan cemetery, Ningxia, China
Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD
Identification of the genetic determinants of shovel-shaped incisors and Carabelli's cusp
| Unique citing works | 76 |
|---|---|
| Citations per year | 3,8 |
| Citation span | 2006 - 2026 (21) |
| Citation velocity | current |
| Highly cited | No |
| Citation types | Neutral: 70 |