The Cancer Genome Atlas

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TCGA Cancers Selected for Study by National Cancer Institute
  
• Using TCGA Data, Resources, and Materials by National Cancer Institute
  

Publications

• "Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons" by Galen F. Gao, Joel S. Parker, et al.
  
• A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
  
• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics by Jianfang Liu, Tara Lichtenberg, et al.
  
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer by Katherine A. Hoadley, Christina Yau, et al.
  
• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
  
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
  
• Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
  
• Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
  
• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas by Theo A. Knijnenburg, Linghua Wang, et al.
  
• Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
  
• Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
  
• Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
  
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation by Tathiane M. Malta, Artem Sokolov, et al.
  
• Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers by Xinxin Peng, Zhongyuan Chen, et al.
  
• Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
  
• Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome Atlas by Franz X. Schaub, Varsha Dhankani, et al.
  
• Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context by Hua-Sheng Chiu, Sonal Somvanshi, et al.
  
• Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
  
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines by Kyle Ellrott, Matthew H. Bailey, et al.
  
• Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep Learning On Pathology Images by Joel Saltz, Rajarsi Gupta, et al.
  
• The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
  
• The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.
  

Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TARGET data matrix by National Cancer Institute
  

Publications

• A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor by Gadd S, Huff V, Walz AL, et al.
  
• Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia by Yang JJ, Cheng C, Devidas M, et al.
  
• Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma by Nakka M, Allen-Rhoades W, Li Y, et al.
  
• CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM by Maxson JE, Ries RE, Wang YC, et al.
  
• Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism by Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, et al.
  
• Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways by Chun HJ, Lim EL, Heravi-Moussavi A, et al.
  
• Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia by Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, et al.
  
• Genomics in childhood acute myeloid leukemia comes of age by Brunner AM, Graubert TA.
  
• Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne et al.
  
• MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia by Lim EL, Trinh DL, Ries RE, et al.
  
• MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours by Perlman EJ, Gadd S, Arold ST, et al.
  
• Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors by Walz AL, Ooms A, Gadd S, et al.
  
• Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations by Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.
  
• Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group by Ooms AH, Gadd S, Gerhard DS, et al.
  
• TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney by Gooskens SL, Gadd S, Guidry Auvil JM, et al.
  
• The genetic landscape of high-risk neuroblastoma by Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, et al.
  
• The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia by Yu Liu, John Easton, Ying Shao, et al.
  
• The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions by Bolouri H, Farrar JE, Triche T Jr, et al.
  

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5, 3.7, 4.0, and 4.2

Tutorials

• DRAGEN Quick Start on AWS by AWS Quick Start Team
  

Tools & Applications

• DRAGEN 3.5.7b Software Release Notes by Illumina Inc.
  
• DRAGEN 3.7.5 Software Release Notes by Illumina Inc.
  
• DRAGEN on BaseSpace Sequence Hub by Illumina Inc.
  
• DRAGEN v4.0.3 Software Release Notes by Illumina Inc.
  
• DRAGEN v4.2.4 Software Release Notes by Illumina Inc.
  
• Illumina Connected Analytics by Illumina Inc.
  
• Illumina Connected Analytics User Guide by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v3.5 User Guide by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v3.7 Online Help by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v4.0 Online Help by Illumina Inc.
  
• Illumina DRAGEN Bio-IT Platform v4.2 Online Help by Illumina Inc.
  
• Nirvana Documentation by Illumina Inc.
  

Publications

• Accurate and efficient calling of small and large variants from popgen datasets using the DRAGEN Bio-IT Platform by Illumina Inc. (2021)
  
• Data solution empowering population genomics by Illumina Inc. (2021)
  
• Demystifying the versions of GRCh38/hg38 reference genomes, how they are used in DRAGEN and their impact on accuracy by Illumina Inc. (2021)
  
• DRAGEN Sets New Standard for Data Accuracy in PrecisionFDA Benchmark Data. Optimizing Variant Calling Performance with Illumina Machine Learning and DRAGEN Graph by Illumina Inc. (2022)
  
• DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2020)
  
• Genotyping variants at population scale using DRAGEN gVCF Genotyper by Illumina Inc. (2023)
  
• Overcoming high homology to detect variation in CYP21A2 with whole-genome sequencing in DRAGEN by Illumina Inc. (2023)
  
• precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions (Preprint) by Olson et al (2020)
  
• Unveiling Illumina Connected Annotations: A breakthrough in genomic annotation by Illumina Inc. (2024)
  

Gabriella Miller Kids First Pediatric Research Program (Kids First)

Tools & Applications

• CAVATICA by Seven Bridges Genomics
  
• Kids First DRC Portal by Kids First DRC
  
• Kids First DRC Source Code by Kids First DRC
  
• PedcBioPortal by cBioPortal
  

Publications

• Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy by Eshini Panditharatna, Lindsay B Kilburn, et al.
  
• Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans. by Mary C Whitman, Noriko Miyake, et al.
  
• Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita. by Suzanna G M Frints, Friederike Hennig, et al.
  
• Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. by Fengqi Chang, Fumin Lin, et al.
  
• Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. by Allison H Seiden, Felix Richter, et al.
  
• Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect by Sherin Shaaban, Sarah MacKinnon et al.
  
• Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. by Madison R Bishop, Kimberly K Diaz Perez, et al.
  
• Genomic Analyses Implicate Noncoding De Novo Variants in Congenital Heart Disease. by Felix Richter, Sarah U Morton, et al.
  
• Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. by Laura Egolf, Zalman Vaksman, et al.
  
• Germline microsatellite genotypes differentiate children with medulloblastoma. by Samuel Rivero-Hinojosa, Nicholas Kinney, et al.
  
• MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance by William B Dobyns, Kimberly A Aldinger, et al.
  
• MAGEL2-Related Disorders: A study and case series. by Jameson Patak, James Gilfert, et al.
  
• Phenotype delineation of ZNF462 related syndrome. by Paul Kruszka, Tommy Hu, et al.
  
• The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. by Deanne M Taylor, Bruce J Aronow, et al.
  
• Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. by Nandita Mukhopadhyay, Madison Bishop, et al.
  

Genome Aggregation Database (gnomAD)

Tools & Applications

• gnomAD quality control GitHub repository by gnomAD Production Team
  
• Hail by Hail Team
  
• Hail utilities for gnomAD by gnomAD Production Team
  

Publications

• A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625, 92–100 (2024) by Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., gnomAD Project Consortium, O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M., MacArthur, D. G. & Karczewski, K. J.
  
• A structural variation reference for medical and population genetics. Nature 581, 444–451 (2020) by Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., Watts, N. A., Solomonson, M., O’Donnell-Luria, A., Baumann, A., Munshi, R., Walker, M., Whelan, C., Huang, Y., Brookings, T., ... Talkowski, M. E.
  
• Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016) by Lek, M., Karczewski, K., Minikel, E. et al.
  
• Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals. Nature Communications 11, 2523 (2020) by Whiffin, N., Karczewski, K. J., Zhang, X., Chothani, S., Smith, M. J., Gareth Evans, D., Roberts, A. M., Quaife, N. M., Schafer, S., Rackham, O., Alföldi, J., O’Donnell-Luria, A. H., Francioli, L. C., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, Cook, S. A., Barton, P. J. R., MacArthur, D. G., & Ware, J. S.
  
• Evaluating potential drug targets through human loss-of-function genetic variation. Nature 581, 459–464 (2020) by Minikel, E. V., Karczewski, K. J., Martin, H. C., Cummings, B. B., Whiffin, N., Rhodes, D., Alföldi, J., Trembath, R. C., van Heel, D. A., Daly, M. J., Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Schreiber, S. L., & MacArthur, D. G.
  
• gnomAD v2.1 by Laurent Francioli, Grace Tiao, Konrad Karczewski, Matthew Solomonson, Nick Watts
  
• gnomAD v3.0 by Laurent Francioli, Daniel MacArthur
  
• Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nature Communications 11, 2539 (2020) by Wang, Q., Pierce-Hoffman, E., Cummings, B. B., Karczewski, K. J., Alföldi, J., Francioli, L. C., Gauthier, L. D., Hill, A. J., O’Donnell-Luria, A. H., Genome Aggregation Database (gnomAD) Production Team, Genome Aggregation Database (gnomAD) Consortium, & MacArthur, D. G.
  
• Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD. bioRxiv (p. 784157) by Karczewski, K. J., Gauthier, L. D., Daly, M. J.
  
• The effect of LRRK2 loss-of-function variants in humans. Nature Medicine (2020) by Whiffin, N., Armean, I. M., Kleinman, A., Marshall, J. L., Minikel, E. V., Goodrich, J. K., Quaife, N. M., Cole, J. B., Wang, Q., Karczewski, K. J., Cummings, B. B., Francioli, L., Laricchia, K., Guan, A., Alipanahi, B., Morrison, P., Baptista, M. A. S., Merchant, K. M., Genome Aggregation Database Production Team, ... MacArthur, D. G.
  
• The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020) by Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., ... MacArthur, D. G.
  
• Transcript expression-aware annotation improves rare variant interpretation. Nature 581, 452–458 (2020) by Cummings, B. B., Karczewski, K. J., Kosmicki, J. A., Seaby, E. G., Watts, N. A., Singer-Berk, M., Mudge, J. M., Karjalainen, J., Kyle Satterstrom, F., O’Donnell-Luria, A., Poterba, T., Seed, C., Solomonson, M., Alföldi, J., The Genome Aggregation Database Production Team, The Genome Aggregation Database Consortium, Daly, M. J., & MacArthur, D. G.
  

The Singapore Nanopore Expression Data Set

Tutorials

• Accessing the SG-NEx dataset on AWS by Ying Chen
  
• Basecalling and analysing SG-NEx samples in S/BLOW5 format by Hasindu Gamaarachchi
  
• Differential RNA modification analysis tutorial with xPore by Yu Song Chuah
  
• Performing transcript discovery and quantification with Bambu by Min Hao Ling
  
• RNA modification analysis tutorial with m6Anet by Yu Song Chuah
  

Tools & Applications

• Bambu: Transcript discovery and quantification using long read RNA-Seq data by Ying Chen, Andre Sim et al.
  
• JAFFAL: Detection of fusion genes from long read RNA-Seq data by Nadia M Davidson et al.
  
• m6Anet: Identification of m6A from a single direct RNA-Seq sample by Christopher Hendra et al.
  
• nf-core/nanoseq: A nanopore DNA and RNA-Seq demultiplexing, QC, alignment and analysis pipeline by Chelsea Sawyer et al.
  
• xPore: Identification of differential RNA modification from direct RNA-Seq data by Ploy Pratanwanich et al.
  

Publications

• A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. by Ying Chen et al.
  
• Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. by Yuk Kei Wan et al.
  
• Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. by Christopher Hendra et al.
  
• Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. by Ploy N Pratanwanich et al.
  
• JAFFAL: Detecting fusion genes with long read transcriptome sequencing. by Nadia M Davidson et al.
  

Garvan Institute Long Read Sequencing Benchmark Data

Tutorials

• Directly processing on an s3fs mount by Hasindu Gamaarachchi
  
• Fetching subsets with slow5curl and samtools by Bonson Wong
  

Tools & Applications

• buttery-eel: The buttery eel - a slow5 guppy basecaller wrapper by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Slow5curl: library and tool for accessing remote BLOW5 files. by Wong, B., et al.
  
• Slow5lib: toolkit slow5lib is a software library for reading & writing SLOW5 files. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Slow5tools: toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  

Publications

• Accelerated nanopore basecalling with SLOW5 data format. by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
  
• Fast nanopore sequencing data analysis with SLOW5. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
  
• Flexible and efficient handling of nanopore sequencing signal data with slow5tools. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
  

PubSeq - Public Sequence Resource

Tutorials

• PubSeq Documentation by PubSeq development team
  
• PubSeq FAQ by PubSeq development team
  
• Query metadata by PubSeq development team
  
• REST API by PubSeq development team
  
• Submitting a sequence by PubSeq development team
  

Tools & Applications

• Source code for (meta)data uploader by PubSeq development team
  
• Source code for CWL workflows by PubSeq development team
  
• Source code for website by PubSeq development team
  

Publications

• Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.
  

Cancer Cell Line Encyclopedia (CCLE)

Tools & Applications

• Broad Institute Cancer Cell Line Encyclopedia by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• Genomic Data Commons by National Cancer Institute
  
• ISB CGC BigQuery tables by Institute for Systems Biology
  

Publications

• Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, M., Huang F. et al.
  
• Pharmacogenomic agreement between two cancer cell line data sets by The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium
  
• The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina Caponigro Stransky et al.
  
• The landscape of cancer cell line metabolism by Li, H. et al.
  

Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET)

Tutorials

• Finding and Downloading TaRGET II Data files by TaRGET-DCC
  

Tools & Applications

• Visualize TaRGET II data with WashU Epigenome Browser by WashU Epigenome Browser
  

Publications

• Comparison of differential accessibility analysis strategies for ATAC-seq data by Gontarz P, Fu S, Xing X, Liu S, Miao B et.al.
  
• Environmental Determinants of cardiovasular disease: lessons learned from air pollution by Al-Kindi SG, Brook RD, Biswal S, Rajagopalan S.
  
• Epigenetic biomarkers and preterm birth by Park B, Khanam R, Vinayachandran V, et.al.
  
• Metabolic effects of air pollution exposure and reversibility by Rajagopalan S, Park B, Palanivel R, et al.
  
• The NIEHS TaRGET II Consortium and environmental epigenomics by Wang, T., Pehrsson, E., Purushotham, D. et al.
  
• The role of environmental exposures and the epigenome in health and disease. by Perera BPU, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC.
  

Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko, Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu, Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine, Richard D. Smith, Daniel W. Chan, Karin D. Rodland, the CPTAC Investigators
  
• Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by Suhas Vasaikar, Chen Huang, Xiaojing Wang. Vladislav A. Petyuk, Sara R. Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman, Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting Wang, Matthew C. Chambers, Robbert J.C. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith, Karin D. Rodland, Daniel C. Liebler, Tao Liu, Bing Zhang, Clinical Proteomic Tumor Analysis Consortium
  
• Proteomic analysis of colon and rectal carcinoma using standard and customized databases by Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC
  

ICGC on AWS

Tutorials

• AWS Pancancer Workflow Launcher by Solomon Shorser
  

Publications

• Analyses of non-coding somatic drivers in 2,693 cancer whole genomes by Rheinbay et al (2020)
  
• Genomic basis of RNA alterations in cancer by PCAWG Transcriptome Core Group et al. (2020)
  
• Pan-cancer analysis of whole genomes by The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020)
  
• Patterns of somatic structural variation in human cancer genomes by Li et al. (2020)
  
• The evolutionary history of 2,658 cancers by Gerstung et al (2020)
  
• The repertoire of mutational signatures in human cancer by Alexandrov et al (2020)
  

Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics by Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H
  
• Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L1, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium
  

Open Bioinformatics Reference Data for Galaxy

Tutorials

• Using Open Bio Ref Data with Galaxy and Bioconductor by Enis Afgan, Alexandru Mahmoud, Nuwan Goonasekera
  

Tools & Applications

• Bioconductor by Bioconductor Project
  
• Galaxy by Galaxy Project
  

Publications

• Accessible, curated metagenomic data through ExperimentHub by Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, and Levi Waldron
  
• TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages by Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D'Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
  
• Wrangling Galaxy's reference data by Daniel Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko
  

Serratus: Ultra-deep Search for Novel Viruses - Versioned Data Release

Tools & Applications

• Serratus Explorer by Serratus Team
  
• Tantalus: An R Package for exploration of Serratus data by Serratus Team
  

Publications

• coronaSPAdes. From biosynthetic gene clusters to RNA viral assemblies by Meleshko D., Hajirasouliha I., and Korobeynikov A. (2021)
  
• Diversification of mammalian deltaviruses by host shifting by Bergner L.M., Orton R.J., et al (2021)
  
• Petabase-scale sequence alignment catalyses viral discovery by Edgar R., Taylor J., Lin V., et al (2021)
  
• Ribovirus classification by a polymerase barcode sequence by Babaian A., and Edgar R. (2021)
  

3000 Rice Genomes Project

Tools & Applications

• RiceGalaxy by International Rice Research Institute
  

Publications

• Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study by Meng B et al (2022)
  
• Rice Galaxy: an open resource for plant science by Juanillas V et al (2019)
  
• Structural variants in 3000 rice genomes by Fuentes RR et al (2019)
  
• Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice by Chen J et al (2019)
  

CoMMpass from the Multiple Myeloma Research Foundation

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• "Identification of Initiating Trunk Mutations and Distinct Molecular Subtypes: An Interim Analysis of the Mmrf Commpass Study" by Jonathan J Keats, PhD, Gil Speyer, Legendre Christophe, Christofferson Austin, Kristi Stephenson, BS, Ahmet Kurdoglu, Megan Russell, Aldrich Jessica, Cuyugan Lori, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, David Siegel, MD PhD, Ravi Vij, MD MBA, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD PhD, Robert M. Rifkin, Norma C Gutierrez, The MMRF CoMMpass Network, Jen Toups, Mary Derome, MS, Winnie Liang, PhD, Seunchan Kim, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Sagar Lonial, MD
  
• "Interim Analysis Of The MMRF CoMMpass Trial: a Longitudinal Study In Multiple Myeloma Relating Clinical Outcomes To Genomic and Immunophenotypic Profiles" by Keats JJ, Craig DW, Liang W, Venkata Y, Kurdoglu A, Aldrich J, Auclair D, Allen K, Harrison B, Jewell S, Kidd PG, Correll M, Jagannath S, Siegel DS, Vij R, Orloff G, Zimmerman TM, MMRF CoMMpass Network, Capone W, Carpten J, Lonial S.
  
• "Interim Analysis of the Mmrf Commpass Trial: Identification of Novel Rearrangements Potentially Associated with Disease Initiation and Progression" by Sagar Lonial, MD, Venkata D Yellapantula, Winnie Liang, PhD, Ahmet Kurdoglu, BS, Jessica Aldrich, MSc, Christophe M. Legendre, MD, Kristi Stephenson, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Megan Russell, Austin Christofferson, Lori Cuyugan, Dan Rohrer, Alex Blanski, Meghan Hodges, Mmrf CoMMpass Network, Mary Derome, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, David Craig, PhD, John Carpten, PhD, Jonathan J. Keats, PhD
  
• "Molecular Predictors of Outcome and Drug Response in Multiple Myeloma: An Interim Analysis of the Mmrf CoMMpass Study" by Jonathan J Keats, PhD, Gil Speyer, Austin Christofferson, Christophe Legendre, PhD, Jessica Aldrich, Megan Russell, Lori Cuyugan, Jonathan Adkins, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, Ravi Vij, MD, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD, Robert M Rifkin, Norma C Gutierrez, MD PhD, Mmrf CoMMpass Network, Jennifer Yesil, MS, Mary Derome, MS, Seungchan Kim, PhD, Winnie Liang, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Daniel Auclair, PhD, Sagar Lonial, MD FACP
  

Logan Unitigs and Contigs of the Sequence Read Archive (SRA) on AWS

Tutorials

• Downloading unitigs of several accessions by Rayan Chikhi
  
• Downloading, mapping many contigs to a gene of interest by Rayan Chikhi
  
• Search for a k-mer of interest inside an unitigs accession by Rayan Chikhi
  

Tools & Applications

• Minia 3 by Rayan Chikhi
  
• Open Virome by Artem Babaian
  

NIH NCBI Sequence Read Archive (SRA) on AWS

Tutorials

• Access SRA data using Amazon Web Services (AWS) by NCBI SRA
  
• Get started with the SRA and Amazon Athena by NCBI SRA
  
• SRA in the Cloud by NCBI SRA
  

Tools & Applications

• SRA Toolkit by NCBI SRA
  

Publications

• The Sequence Read Archive by Leinonen et al (2011)
  

Basic Local Alignment Sequences Tool (BLAST) Databases

Tools & Applications

• BLAST on the Cloud with NCBI’s ElasticBLAST by Sixing Huang
  
• BLAST+ Docker by NCBI BLAST
  

Publications

• BLAST+: Architecture and Applications by Christiam Camacho 1 , George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden
  
• Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs by S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman
  

Encyclopedia of DNA Elements (ENCODE)

Tutorials

• ENCODE CTCF ChIP-seq data correlation across different cell types by Paul Sud
  
• Exploring ENCODE data from EC2 with Jupyter notebook by Keenan Graham
  
• Ingesting ENCODE data into TileDB with S3 backend by Otto Jolanki
  

Publications

• New developments on the Encyclopedia of DNA Elements (ENCODE) data portal by Luo et al 2020
  

Genome in a Bottle on AWS

Tools & Applications

• GA4GH Benchmarking Tools by GA4GH Benchmarking Team
  
• The Genome in a Bottle Github Project by Genome In A Bottle Consortium
  

Publications

• Extensive sequencing of seven human genomes to characterize benchmark reference materials by Zook J et al (2016)
  
• High-coverage, long-read sequencing of Han Chinese trio reference samples by Wang Y et al (2019)
  

Molecular Profiling to Predict Response to Treatment (phs001965)

Tools & Applications

• Childhood Cancer Data Initiative Data Catalog by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• Finding the way to Wilms tumor by comparing the primary and relapse tumor samples by Filippo Spreafico, Sara Ciceri, et al.
  
• Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study by Samantha Gadd, Vicki Huff, et al.
  

Refgenie reference genome assets

Tutorials

• Basic Refgenie tutorial by Nathan Sheffield
  

Tools & Applications

• Pipeline for ATAC-seq data analysis by Jason Smith and Nathan Sheffield
  
• Pipeline for PRO-seq data analysis by Jason Smith and Nathan Sheffield
  

Publications

• Refgenie: a reference genome resource manager by Michał Stolarczyk, Vincent P Reuter, Jason P Smith, Neal E Magee, Nathan C Sheffield
  

UK Biobank Linkage Disequilibrium Matrices

Tutorials

• PolyFun Wiki by Omer Weissbrod
  

Tools & Applications

• PolyFun and PolyPred software by Omer Weissbrod
  

Publications

• Functionally informed fine-mapping and polygenic localization of complex trait heritability by Weissbrod et al.
  
• Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores by Weissbrod et al.
  

UK Biobank Pan-Ancestry Summary Statistics

Tutorials

• Hail Tutorials by Hail Team
  

Tools & Applications

• Hail by Hail Team
  
• Hail on AWS Quick Start by Amazon Web Services and PrivoIT
  

Publications

• Pan-ancestry genetic analysis of the UK Biobank by Pan UKBB Team
  

Beat Acute Myeloid Leukemia (AML) 1.0

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms by Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, et al.
  
• Functional Genomic Landscape of Acute Myeloid Leukemia by Jeffrey W. Tyner, Cristina E. Tognon, Dan Bottomly et al.
  

Broad Genome References

Tutorials

• Using Amazon FSx for Lustre for Genomics Workflows on AWS by W. Lee Pang
  BatchFSx

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Publications

• Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA by Willey J. C., Morrison T. B., Austermiller B., Crawford E. E., et al (2021)
  

Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• A multiprotein supercomplex controlling oncogenic signalling in lymphoma by Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL 3rd, Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M, Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM
  
• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., Calvin A. Johnson, Ph.D., James D. Phelan, Ph.D., James Q. Wang, Ph.D., Sandrine Roulland, Ph.D., Monica Kasbekar, Ph.D., Ryan M. Young, Ph.D., Arthur L. Shaffer, Ph.D., Daniel J. Hodson, M.D., Ph.D., Wenming Xiao, Ph.D., et al.
  

Exceptional Responders Initiative

Tools & Applications

• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study by Barbara A. Conley, Lou Staudt, et al.
  

Foundation Medicine Adult Cancer Clinical Dataset (FM-AD)

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis by Ryan J. Hartmaier, Lee A. Albacker, Juliann Chmielecki, Mark Bailey, Jie He, Michael E. Goldberg, Shakti Ramkissoon, James Suh, Julia A. Elvin, Samuel Chiacchia, Garrett M. Frampton, Jeffrey S. Ross, Vincent Miller, Philip J. Stephens and Doron Lipson
  
• Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. by Beltran H, Yelensky R, Frampton GM, Park K, Downing SR, MacDonald TY, Jarosz M, Lipson D, Tagawa ST, Nanus DM, Stephens PJ, Mosquera JM, Cronin MT, Rubin MA
  

NASA Space Biology Open Science Data Repository (OSDR)

Publications

• Advancing the Integration of Biosciences Data Sharing to Further Enable Space Exploration by Ryan T. Scott, Kirill Grigorev, Graham Mackintosh, Samrawit G. Gebre, Christopher E. Mason, Martha E. Del Alto, Sylvain V. Costes
  
• GeneLab: Omics database for spaceflight experiments by Shayoni Ray, Samrawit Gebre, Homer Fogle, Daniel C Berrios, Peter B Tran, Jonathan M Galazka, Sylvain V Costes
  
• NASA GeneLab: interfaces for the exploration of space omics data by Daniel C Berrios, Jonathan Galazka, Kirill Grigorev, Samrawit Gebre, Sylvain V Costes
  

QIIME 2 Tutorial Data

Tutorials

• Developing with QIIME 2 by Caporaso and Bolyen
  
• QIIME 2 User Documentation (currently being replaced by *Using QIIME 2*) by The QIIME 2 Development Team
  
• Using QIIME 2 by Caporaso Lab
  

The Human Microbiome Project

Publications

• New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract by Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al
  
• Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
  
• The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
  

Variant Effect Predictor (VEP) and the Loss-Of-Function Transcript Effect Estimator (LOFTEE) Plugin

Tools & Applications

• Hail by Neale Lab
  
• Loss-Of-Function Transcript Effect Estimator (LOFTEE) by Konrad Karczewski
  
• Variant Effect Predictor (VEP) by Ensembl
  

4D Nucleome (4DN)

Tutorials

• Finding and Downloading 4DN Data files by 4DN-DCIC
  
• Using jupyterhub on the 4DN data portal by 4DN-DCIC
  

Cancer Genome Characterization Initiatives - Burkitt Lymphoma, HIV+ Cervical Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma by Grande B. M., Gerhard D. S., Jiang A., Griner N. B., Abramson J. S., Alexander T. B., et al.
  

Cloud Indexes for Bowtie, Kraken, HISAT, and Centrifuge

Tutorials

• Table of contents for tutorials for constituent tools by Ben Langmead
  

Publications

• Reducing reference bias using multiple population reference genomes by Chen et al (2020)
  

DNAStack COVID19 SRA Data

Tutorials

• Viral lineage assignment by Heather Ward
  BatchEC2S3

Tools & Applications

• Viral AI by DNAstack
  

GATK Structural Variation (SV) Data

Tutorials

• AWS Setup & Execution by Goldfinch Bio and Loka Inc.
  

Tools & Applications

• Structural Variant Analysis on AWS with Amazon FSx for Lustre by Goldfinch Bio and Loka Inc.
  

Genomic Characterization of Metastatic Castration Resistant Prostate Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic characterization of metastatic castration-resistant prostate cancer patients undergoing PSMA radioligand therapy: A single-center experience by Swayamjeet Satapathy, Chandan K Das, et al.
  

Hecatomb Databases

Tutorials

• The Hecatomb Tutorial by Michael Roach
  

Publications

• No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study by Michael Roach,Adrian Cantu,Melissa Krizia Vieri,Matthew Cotten,Paul Kellam,My Phan,Lia van der Hoek,Michel Mandro,Floribert Tepage,Germain Mambandu,Gisele Musinya,Anne Laudisoit,Robert Colebunders,Robert Edwards, John L. Mokili
  

Indexes for Kaiju

Tutorials

• Quickstart Tutorial for downloading the index files and running Kaiju. by Peter Menzel
  

Publications

• Fast and sensitive taxonomic classification for metagenomics with Kaiju by Peter Menzel et al (2016)
  

Integrative Analysis of Lung Adenocarcinoma in Environment and Genetics Lung cancer Etiology (Phase 2)

Tools & Applications

• EAGLE - Environment And Genetics in Lung cancer Etiology by National Cancer Institute Division of Cancer Epidemiology and Genetics
  
• Genomic Data Commons by National Cancer Institute
  

National Cancer Institute Center for Cancer Research - Diffuse Large B Cell Lymphoma (DLBCL) Genomics and Expression

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., et al.
  

OpenCRAVAT

Tutorials

• Changing the OpenCRAVAT store url by Kyle Moad
  

Tools & Applications

• OpenCRAVAT by Karchinlab
  

Oregon Health & Science University Chronic Neutrophilic Leukemia Dataset

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic landscape of neutrophilic leukemias of ambiguous diagnosis by Zhang H, Wilmot B, Bottomly D et al.
  

Pancreatic Cancer Organoid Profiling

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer by Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TD, et al.
  

1000 Genomes

Publications

• Exploratory data analysis of genomic datasets using ADAM and Mango with Apache Spark on Amazon EMR by Alyssa Marrow
  

CIViC (Clinical Interpretation of Variants in Cancer)

Publications

• CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Malachi Griffith
  

COVID-19 Genome Sequence Dataset

Tools & Applications

• Download SRA sequence data using Amazon Web Services (AWS) by NCBI SRA
  

GATK Test Data

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Human Cancer Models Initiative (HCMI) Cancer Model Development Center

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Human PanGenomics Project

Publications

• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes by Shafin et al (2020)
  

Oxford Nanopore Technologies Benchmark Datasets

Tutorials

• ONT Dataset Tutorials by EPI2MELabs
  

Synthea Coherent Data Set

Publications

• The “Coherent Data Set”: Combining Patient Data and Imaging in a Comprehensive Synthetic Health Record. by Walonoski J, Hall D, Bates KM, Farris MH, Dagher J, Downs ME, Sivek RT, Wellner B, Gregorowicz A, Hadley M, Campion FX, Levine L, Wacome K, Emmer G, Kemmer A, Malik M, Hughes J, Granger E, Russell S.
  

Tabula Muris

Publications

• Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. by Tabula Muris Consortium (2019)
  

Tabula Muris Senis

Tutorials

• Fast queries of scRNAseq datasets with Amazon Athena by Andrew Ang, James Golden, Lisa McFerrin, and Lee Pang
  AthenaGlue

Tabula Sapiens

Publications

• The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans by The Tabula Sapiens Consortium, Stephen R Quake
  

iHART Whole Genome Sequencing Data Set

Publications

• Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks by Ruzzo et al. (2020)
  

recount3

Tutorials

• recount3 quick start guide by Leonardo Collado-Torres
  

SocialGene RefSeq Databases

Tutorials

• How to use SocialGene on AWS by Chase M. Clark
  EC2

Tools & Applications

• socialgene on pypi.python.org - python module for creating and interacting with SocialGene Neo4j databases by Chase M. Clark
  

Publications

• Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene. by C. M. Clark, J. C. Kwan
  

Platinum Pedigree

Publications

• A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree by Porubsky et. al.
  
• The Platinum Pedigree: A long-read benchmark for genetic variants by Kronenberg et. al.
  

AWS iGenomes

Tools & Applications

• nf-core analysis pipelines by Phil Ewels
  

Google Brain Genomics Sequencing Dataset for Benchmarking and Development

Publications

• An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development by Baid G., Nattestad M., Kolesnikov A., Goel S., Yang H., Chang P., and Carroll A (2020)