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The Sequence Alignment/Map format and SAMtools
Open accessAbstract
SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.
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“Mapping reads to specific genes is relatively straightforward with the bioinformatics tools available today [10-13], but using these tools to distinguish between reads derived from alternative alleles of the same gene remains challenging [9].”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [13]
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“Droplet single cell RNA-sequencing (dscRNA-seq) has increased substantially the throughput of single cell capture and library preparation1, 10, enabling the simultaneous profiling of thousands of cells.”
From Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2018) · cites this paper as [10]
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“While strategies to demultiplex cells from different species1, 10, 17 or host and graft samples17 have been reported, simultaneously demultiplexing and detecting doublets from more than two individuals has not been possible.”
From Multiplexed droplet single-cell RNA-sequencing using natural genetic variation (2018) · cites this paper as [10]
Experimental — accuracy not yet measuredIn the citing paper
“After the Trimmmed Mean of M-values (TMM)55 and limma-voom normalization, we found that samples A and B were well distinguished by multidimensional scaling (Supplementary Fig. 21d), and that the two replicates with abnormal GC content distributions (PGM1.A.4 and PGM2.A.2) were separated from the other replicates of sample A at dimension 2.”
From Detecting and correcting systematic variation in large-scale RNA sequencing data (2014) · cites this paper as [55]
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“Only uniquely mapped reads were retained, and the alignments were subsequently filtered using the SAMtools package (v0.1.19)88 to remove duplicate reads.”
From Epigenetic regulation of brain region-specific microglia clearance activity (2018) · cites this paper as [88]
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“We evaluated the potential of whole genome imputation to infer diploid genotypes from low-coverage genomes by randomly subsampling our high-coverage genomes (NE1 and BR2) to a series of coverages ranging from 0.1 to 5 × using SAMtools45”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [45]
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638
Self-citationNext-Generation DNA Sequencing Methods
Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,469
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Items 101–200 of 1,739
Accurate detection of complex structural variations using single-molecule sequencing
Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., & Schatz, M. C. (2018) · Nature Methods · doi:10.1038/s41592-018-0001-7 · Cited by 1,601
On the origin and continuing evolution of SARS-CoV-2
Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa036 · Cited by 1,627
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., & Cheetham, R. K. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts271 · Cited by 1,589
The origin and evolution of mutations in acute myeloid leukemia
Welch, J. S., Ley, T. J., Link, D. C., Miller, C. A., Larson, D. E., Koboldt, D. C., Wartman, L. D., Lamprecht, T. L., Liu, F., Xia, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.023 · Cited by 1,575
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
Franzén, O., Gan, L.-M., & Björkegren, J. L. M. (2019) · Database · doi:10.1093/database/baz046 · Cited by 1,551
Whole–genome characterization of chemoresistant ovarian cancer
Patch, A., Christie, E. L., Etemadmoghadam, D., Garsed, D. W., George, J., Fereday, S., Nones, K., Cowin, P. A., Alsop, K., Bailey, P. J., et al. (2015) · Nature · doi:10.1038/nature14410 · Cited by 1,572
Population genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550
ART: a next-generation sequencing read simulator
Huang, W., Li, L., Myers, J. R., & Marth, G. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr708 · Cited by 1,548
Self-citationSaam, J. R., Arnell, C., Theisen, A. P., Moyes, K., Marino, I., Roundy, K. M., & WENSTRUP, R. J. (2015) · Oncology · doi:10.1159/000437307 · Cited by 1,533
Finotello, F., Mayer, C., Plattner, C., Laschober, G. T., Rieder, D., Hackl, H., Krogsdam, A., Loncová, Z., Posch, W., Wilflingseder, D., et al. (2019) · Genome Medicine · doi:10.1186/s13073-019-0638-6 · Cited by 1,550
Genome-wide patterns of selection in 230 ancient Eurasians
Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. (2015) · Nature · doi:10.1038/nature16152 · Cited by 1,515
LUMPY: a probabilistic framework for structural variant discovery
Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,544
Identification of the tumour transition states occurring during EMT
Pastushenko, I., Brisebarre, A., Sifrim, A., Fioramonti, M., Revenco, T., Boumahdi, S., Keymeulen, A. V., Brown, D. V., Moers, V., Lemaire, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0040-3 · Cited by 1,556
Takagi, H., Abe, A., Yoshida, K., Kosugi, S., Natsume, S., Mitsuoka, C., Uemura, A., Utsushi, H., Tamiru, M., Takuno, S., et al. (2013) · The Plant Journal · doi:10.1111/tpj.12105 · Cited by 1,485
Prevalence and architecture of de novo mutations in developmental disorders
Study, D. D. D. (2017) · Nature · doi:10.1038/nature21062 · Cited by 1,480
Landscape of Microsatellite Instability Across 39 Cancer Types
Bonneville, R., Krook, M. A., Kautto, E. A., Miya, J., Wing, M. R., Chen, H., Reeser, J. W., Yu, L., & Roychowdhury, S. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00073 · Cited by 1,505
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
Koike, N., Yoo, S.-H., Huang, H.-C., Kumar, V., Lee, C., Kim, T.-K., & Takahashi, J. S. (2012) · Science · doi:10.1126/science.1226339 · Cited by 1,464
Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin
Snyder, M. W., Kircher, M., Hill, A. J., Daza, R. M., & Shendure, J. (2016) · Cell · doi:10.1016/j.cell.2015.11.050 · Cited by 1,492
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Li, H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw152 · Cited by 1,500
Self-citationBlanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
Next-Generation Digital Information Storage in DNA
Church, G. M., Gao, Y., & Kosuri, S. (2012) · Science · doi:10.1126/science.1226355 · Cited by 1,441
Feldgarden, M., Brover, V. V., Haft, D. H., Prasad, A. B., Slotta, D. J., Tolstoy, I., Tyson, G. H., Zhao, S., Hsu, C.-H., McDermott, P. F., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00483-19 · Cited by 1,459
Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak
Zhang, T., Wu, Q., & Zhang, Z. (2020) · Current Biology · doi:10.1016/j.cub.2020.03.022 · Cited by 1,397
Genotype and SNP calling from next-generation sequencing data
Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2986 · Cited by 1,396
Joensen, K., Scheutz, F., Lund, O., Hasman, H., Kaas, R. S., Nielsen, E. M., & Aarestrup, F. M. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.03617-13 · Cited by 1,394
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data
Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D. (2017) · eLife · doi:10.7554/elife.26476 · Cited by 1,389
Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia
Yankova, E., Blackaby, W., Albertella, M. R., Rak, J. M., Braekeleer, E. D., Tsagkogeorga, G., Pilka, E. S., Aspris, D., Leggate, D., Hendrick, A. G., et al. (2021) · Nature · doi:10.1038/s41586-021-03536-w · Cited by 1,391
A unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357
Self-citationGenome sequencing reveals agronomically important loci in rice using MutMap
Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., Yoshida, K., Mitsuoka, C., Tamiru, M., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2095 · Cited by 1,350
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
Kang, H. M., Subramaniam, M., Targ, S., Nguyen, M., Maliskova, L., McCarthy, E., Wan, E., Wong, S., Byrnes, L., Lanata, C. M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4042 · Cited by 1,101
“Inspired by models and algorithms developed for detecting contamination in DNA sequencing 18 , demuxlet is fast, accurate, scalable, and compatible with standard input formats 17, 19, 20 .”
MethodParental olfactory experience influences behavior and neural structure in subsequent generations
Dias, B. G., & Ressler, K. J. (2014) · Nature Neuroscience · doi:10.1038/nn.3594 · Cited by 1,338
Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong, C. H., Khor, C. C., Petric, R., Hibberd, M. L., & Nagarajan, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks918 · Cited by 1,370
Performance comparison of benchtop high-throughput sequencing platforms
Loman, N. J., Misra, R., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. R., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,383
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Haroon, M. F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., Yuan, Z., & Tyson, G. W. (2013) · Nature · doi:10.1038/nature12375 · Cited by 1,364
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayır, A., Bakkaloğlu, A., Özen, S., Sanjad, S. A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,385
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314
A reference genome for common bean and genome-wide analysis of dual domestications
Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J. W., Shu, S., Song, Q., Chavarro, C. M., et al. (2014) · Nature Genetics · doi:10.1038/ng.3008 · Cited by 1,347
Lischer, H. E. L., & Excoffier, L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr642 · Cited by 1,300
Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292
Personal omics profiling reveals dynamic molecular and medical phenotypes
Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
Moreno-Mateos, M. A., Vejnar, C. E., Beaudoin, J.-D., Fernandez, J. P., Mis, E. K., Khokha, M. K., & Giraldez, A. J. (2015) · Nature Methods · doi:10.1038/nmeth.3543 · Cited by 1,290
Genomic spectra of biliary tract cancer
Nakamura, H. K., Arai, Y., Totoki, Y., Shirota, T., Elzawahry, A., Kato, M., Hama, N., Hosoda, F., Urushidate, T., Ohashi, S., et al. (2015) · Nature Genetics · doi:10.1038/ng.3375 · Cited by 1,306
Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting
Matsushita, H., Vesely, M. D., Koboldt, D. C., Rickert, C. G., Uppaluri, R., Magrini, V. J., Arthur, C. D., White, J. M., Chen, Y.-S., Shea, L. K., et al. (2012) · Nature · doi:10.1038/nature10755 · Cited by 1,285
N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells
Wang, Y., Li, Y., Toth, J. I., Petroski, M. D., Zhang, Z., & Zhao, J. C. (2014) · Nature Cell Biology · doi:10.1038/ncb2902 · Cited by 1,296
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
Varshney, R. K., Song, C., Saxena, R. K., Azam, S., Sheng, Y., Sharpe, A., Cannon, S. B., Baek, J., Rosen, B. D., Tar’an, B., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2491 · Cited by 1,302
Olson, R., Assaf, R., Brettin, T. S., Conrad, N. R., Cucinell, C. A., Davis, J. J., Dempsey, D. M., Dickerman, A., Dietrich, E. M., Kenyon, R. W., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1003 · Cited by 1,342
Aligning Short Sequencing Reads with Bowtie
Langmead, B. (2010) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1107s32 · Cited by 1,270
BigWig and BigBed: enabling browsing of large distributed datasets
Kent, W. J., Zweig, A. S., Barber, G. P., Hinrichs, A. S., & Karolchik, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq351 · Cited by 1,268
Mapping RNA‐seq Reads with STAR
Dobin, A., & Gingeras, T. (2015) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1114s51 · Cited by 1,265
Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics
Rochette, N. C., Rivera‐Colón, A. G., & Catchen, J. (2019) · Molecular Ecology · doi:10.1111/mec.15253 · Cited by 1,265
CPGAVAS2, an integrated plastome sequence annotator and analyzer
Shi, L., Chen, H., Jiang, M., Wang, L., Wu, X., Huang, L., & Liu, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz345 · Cited by 1,279
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
Toy, W., Shen, Y., Won, H. H., Green, B., Sakr, R. A., Will, M., Li, Z., Gala, K. P., Fanning, S. W., King, T. A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2822 · Cited by 1,280
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
The Tabula Muris Consortium, Almanzar, N., Antony, J., Baghel, A. S., Bakerman, I., Bansal, I., Barres, B. A., Beachy, P. A., Berdnik, D., Bilen, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2496-1 · Cited by 1,247
Yates, A. D., Akanni, W. A., Amode, M. R., Barrell, D. G., Billis, K., Carvalho‐Silva, D., Cummins, C. A., Clapham, P., Fitzgerald, S. F., Gil, L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1157 · Cited by 1,246
Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., & Weissman, J. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.086 · Cited by 1,280
CEL-seq: single-cell RNA-seq by multiplexed linear amplification
Hashimshony, T., Wagner, F., Sher, N., & Yanai, I. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.003 · Cited by 1,231
The chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230
Shankman, L. S., Gomez, D., Cherepanova, O. A., Salmon, M., Alencar, G. F., Haskins, R. M., Swiatlowska, P., Newman, A. A. C., Greene, E. S., Straub, A. C., et al. (2015) · Nature Medicine · doi:10.1038/nm.3866 · Cited by 1,218
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
Tirosh, I., Venteicher, A. S., Hebert, C. M., Escalante, L. E., Patel, A. P., Yizhak, K., Fisher, J. M., Rodman, C., Mount, C., Filbin, M. G., et al. (2016) · Nature · doi:10.1038/nature20123 · Cited by 1,245
BCG Educates Hematopoietic Stem Cells to Generate Protective Innate Immunity against Tuberculosis
Kaufmann, E., Sanz, J., Dunn, J. L., Khan, N., Mendonça, L. E., Pacis, A., Tzelepis, F., Pernet, E., Dumaine, A., Grenier, J.-C., et al. (2018) · Cell · doi:10.1016/j.cell.2017.12.031 · Cited by 1,191
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.835 · Cited by 1,203
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08853-3 · Cited by 1,199
Improved maize reference genome with single-molecule technologies
Jiao, Y., Peluso, P. S., Shi, J., Liang, T. Y., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C.-S., et al. (2017) · Nature · doi:10.1038/nature22971 · Cited by 1,233
A reference map of the human binary protein interactome
Luck, K., Kim, D.-K., Lambourne, L., Spirohn, K., Begg, B. E., Bian, W., Brignall, R., Cafarelli, T., Campos-Laborie, F. J., Charloteaux, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2188-x · Cited by 1,197
Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
Krauthammer, M., Kong, Y., Ha, B. H., Evans, P., Bacchiocchi, A., McCusker, J. P., Cheng, E., Davis, M. J., Goh, G., Choi, M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2359 · Cited by 1,191
Carver, T. J., Harris, S. R., Berriman, M., Parkhill, J., & Keane, J. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr703 · Cited by 1,228
Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2017.066 · Cited by 1,190
Arts, R. J. W., Moorlag, S. J. C. F. M., Novakovic, B., Li, Y., Wang, S.-Y., Oosting, M., Kumar, V., Xavier, R. J., Wijmenga, C., Joosten, L. A. B., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2017.12.010 · Cited by 1,217
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J. W., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.030 · Cited by 1,201
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
Carrión, V. J., Pérez‐Jaramillo, J. E., Cordovez, V., Tracanna, V., de Hollander, M., Ruiz-Buck, D., Mendes, L. W., van IJcken, W. F. J., Expósito, R. G., Elsayed, S. S., et al. (2019) · Science · doi:10.1126/science.aaw9285 · Cited by 1,193
The genetic landscape of high-risk neuroblastoma
Pugh, T. J., Morozova, O., Attiyeh, E. F., Asgharzadeh, S., Wei, J. S., Auclair, D., Carter, S. L., Cibulskis, K., Hanna, M., Kieżun, A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2529 · Cited by 1,198
Circlator: automated circularization of genome assemblies using long sequencing reads
Hunt, M., Silva, N. H. D., Otto, T. D., Parkhill, J., Keane, J. A., & Harris, S. R. (2015) · Genome biology · doi:10.1186/s13059-015-0849-0 · Cited by 1,181
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Meng, G., Li, Y., Yang, C., & Liu, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz173 · Cited by 1,194
Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer
García-Murillas, I., Schiavon, G., Weigelt, B., Ng, C. K. Y., Hrebien, S., Cutts, R. J., Cheang, M. C. U., Osin, P., Nerurkar, A. Y., Kozarewa, I., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aab0021 · Cited by 1,174
GFF Utilities: GffRead and GffCompare
Pertea, G., & Pertea, M. (2020) · F1000Research · doi:10.12688/f1000research.23297.2 · Cited by 1,152
Jacob, F., Salinas, R. D., Zhang, D. Y., Nguyen, P. T. T., Schnoll, J. G., Wong, S. Z. H., Thokala, R., Sheikh, S., Saxena, D., Prokop, S., et al. (2020) · Cell · doi:10.1016/j.cell.2019.11.036 · Cited by 1,149
Mosdepth: quick coverage calculation for genomes and exomes
Pedersen, B. S., & Quinlan, A. R. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx699 · Cited by 1,149
A rapid and robust method for single cell chromatin accessibility profiling
Chen, X., Miragaia, R. J., Natarajan, K. N., & Teichmann, S. A. (2018) · Nature Communications · doi:10.1038/s41467-018-07771-0 · Cited by 1,147
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Ma, S., Zhang, B., LaFave, L. M., Earl, A. S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V. K., Tay, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.056 · Cited by 1,146
Activating ESR1 mutations in hormone-resistant metastatic breast cancer
Robinson, D. R., Wu, Y.-M., Vats, P., Su, F., Lonigro, R. J., Cao, X., Kalyana-Sundaram, S., Wang, R., Ning, Y., Hodges, L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2823 · Cited by 1,145
Comparison of Sequencing Utility Programs
Aronesty, E. (2013) · The Open Bioinformatics Journal · doi:10.2174/1875036201307010001 · Cited by 1,144
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers
Govindan, R., Ding, L., Griffith, M., Subramanian, J., Dees, N. D., Kanchi, K., Maher, C. A., Fulton, R. S., Fulton, L., Wallis, J. W., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.024 · Cited by 1,161
Uncovering the roles of rare variants in common disease through whole-genome sequencing
Cirulli, E. T., & Goldstein, D. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2779 · Cited by 1,136
Qualimap: evaluating next-generation sequencing alignment data
García-Alcalde, F., Okonechnikov, K., Carbonell‐Caballero, J., Cruz, L. M., Götz, S., Tarazona, S., Dopazo, J., Meyer, T. F., & Conesa, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts503 · Cited by 1,135
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
“3.1), (Li et al., 2009).”
InfluentialCount-based differential expression analysis of RNA sequencing data using R and Bioconductor
Anders, S., McCarthy, D. J., Chen, Y., Okoniewski, M. J., Smyth, G. K., Huber, W. K., & Robinson, M. D. (2013) · Nature Protocols · doi:10.1038/nprot.2013.099 · Cited by 1,170
Habermann, A. C., Gutierrez, A. J., Bui, L. T., Yahn, S. L., Winters, N. I., Calvi, C. L., Peter, L., Chung, M.-I., Taylor, C. J., Jetter, C., et al. (2020) · Science Advances · doi:10.1126/sciadv.aba1972 · Cited by 1,129
Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria
Amin, S. A., Hmelo, L. R., van Tol, H. M., Durham, B. P., Carlson, L. T., Heal, K. R., Morales, R. L., Berthiaume, C. T., Parker, M. S., Djunaedi, B., et al. (2015) · Nature · doi:10.1038/nature14488 · Cited by 1,125
Toward almost closed genomes with GapFiller
Boetzer, M., & Pirovano, W. (2012) · Genome biology · doi:10.1186/gb-2012-13-6-r56 · Cited by 1,123
Variant Review with the Integrative Genomics Viewer
Robinson, J., Thorvaldsdóttir, H., Wenger, A. M., Zehir, A., & Mesirov, J. P. (2017) · Cancer Research · doi:10.1158/0008-5472.can-17-0337 · Cited by 1,144
Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
de Bruin, E. C., McGranahan, N., Mitter, R., Salm, M., Wedge, D. C., Yates, L., Jamal-Hanjani, M., Shafi, S., Murugaesu, N., Rowan, A. J., et al. (2014) · Science · doi:10.1126/science.1253462 · Cited by 1,117
Advances in understanding cancer genomes through second-generation sequencing
Meyerson, M. M., Gabriel, S., & Getz, G. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,142
The whole-genome landscape of medulloblastoma subtypes
Northcott, P. A., Buchhalter, I., Morrissy, A. S., Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., et al. (2017) · Nature · doi:10.1038/nature22973 · Cited by 1,112
Zhao, Z., Zhang, K., Wang, Q., Li, G., Zeng, F., Zhang, Y., Wu, F., Chai, R., Wang, Z., Zhang, C., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.10.005 · Cited by 1,113
TOX is a critical regulator of tumour-specific T cell differentiation
Scott, A. C., Dündar, F., Zumbo, P., Chandran, S. S., Klebanoff, C. A., Shakiba, M., Trivedi, P., Menocal, L., Appleby, H., Camara, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1324-y · Cited by 1,106
Genetic and functional drivers of diffuse large B cell lymphoma
Reddy, A., Zhang, J., Davis, N. S., Moffitt, A. B., Love, C. L., Waldrop, A., Leppa, S., Pasanen, A., Meriranta, L., Karjalainen-Lindsberg, M.-L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.027 · Cited by 1,104
Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., Yu, Y., Shu, L., Zhao, Y., Ma, Y., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3096 · Cited by 1,119
Metadata
- Authors
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup
- Affiliations
- Boston College (US)
- 1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org
- Corresponding author
- Durbin, Richard
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-08
- Volume
- 25
- Issue
- 16
- Pages
- 2078-2079
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2723002
- OpenAlex
- W2108234281
- Cited by
- 62,041
- References
- 4
- Citations by year
- 2026: 4515 · 2025: 5629 · 2024: 6225 · 2023: 5854 · 2022: 6476 · 2021: 7180 · 2020: 5531 · 2019: 4365 · 2018: 3577 · 2017: 3034 · 2016: 2584 · 2015: 2289 · 2014: 1917 · 2013: 1350 · 2012: 853
- FWCI
- 194.13
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (077192/Z/05/Z)
- National Institutes of Health (077192)
- National Human Genome Research Institute (U54HG002750, R01HG004719)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- SAMtools, variant calling, 1000 Genomes Project, long reads
- MeSH terms
- Algorithms, Base Sequence, Molecular Sequence Data, Software, Sequence Alignment, Genome, Sequence Analysis, DNA, Computational Biology, Genomics
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