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.
  

Cell Painting Gallery

Tutorials

• Cell Painting wiki by Multiple Authors
  
• Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares by Multiple Authors
  
• Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer by Multiple Authors
  
• Image-based profiling introductory exercise - data and an exercise on exploring image-based profiles, including understanding the various data levels by Beth Cimini
  
• Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition by Multiple Authors
  

Tools & Applications

• Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar
  
• Deep Profiler - Morphological profiling using deep learning by Multiple Authors
  
• Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure by Multiple Authors
  
• Image-based Profiling Recipe by Multiple Authors
  
• Pycytominer - Data processing functions for profiling perturbations by Multiple Authors
  

Publications

• A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
  
• Cell Painting predicts impact of lung cancer variants by Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S
  
• Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes by Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
  
• Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects by Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
  
• Multiplex Cytological Profiling Assay to Measure Diverse Cellular States by Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
  
• Systematic morphological profiling of human gene and allele function via Cell Painting by Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
  
• Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA
  

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.
  

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.
  

CIViC (Clinical Interpretation of Variants in Cancer)

Tutorials

• Introduction to Clinical Interpretation of Somatic Cancer Variants by The Griffith Lab
  

Tools & Applications

• CIViCpy - an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase by The CIViCpy Team
  

Publications

• A community approach to the cancer-variant-interpretation bottleneck by Kilannin Krysiak et al.
  
• CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Malachi Griffith et al.
  
• CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase by Kilannin Krysiak et al.
  
• CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase by Alex H Wagner et al.
  
• Standard operating procedure for curation and clinical interpretation of variants in cancer by Arpad M Danos et al.
  

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)
  

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 sequences inside unitigs or contigs by Rayan Chikhi
  

Tools & Applications

• f2sz by Anton Korobeynikov
  
• Logan Search by Pierre Peterlongo
  
• Minia 3 by Rayan Chikhi
  
• Open Virome by Artem Babaian
  

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
  

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)
  

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
  

Allen Ivy Glioblastoma Atlas

Tutorials

• Accessing Ivy Glioblastoma Atlas Project data by Allen Institute for Brain Science
  

Tools & Applications

• Ivy Glioblastoma Atlas Project by Allen Institute for Brain Science
  

Publications

• An anatomic transcriptional atlas of human glioblastoma by Ralph Puchalski, et al.
  

Allen Mouse Brain Atlas

Tutorials

• Accessing Allen Mouse Brain Atlas data by Allen Institute for Brain Science
  

Tools & Applications

• Allen Mouse Brain Atlas by Allen Institute for Brain Science
  

Publications

• Genome-wide atlas of gene expression in the adult mouse brain by Ed Lein, et al.
  

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
  AWS BatchAmazon FSx

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)
  

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
  

1000 Genomes

Tools & Applications

• Examine genomic variation across populations with AWS by Konstantinos Tzouvanas
  

Publications

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

4D Nucleome (4DN)

Tutorials

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

Biological and Physical Sciences (BPS) Microscopy Benchmark Training Dataset

Publications

• Dose, LET and Strain Dependence of Radiation-Induced 53BP1 Foci in 15 Mouse Strains Ex Vivo Introducing Novel DNA Damage Metrics by Sébastien Penninckx, Egle Cekanaviciute, Charlotte Degorre, Elodie Guiet, Louise Viger, Stéphane Lucasb, Sylvain V. Costes
  
• NASA SMD AI Workshop Report by SMD Artificial Intelligence (AI) Initiative
  

Biological and Physical Sciences (BPS) RNA Sequencing Benchmark Training Dataset

Publications

• Adversarial generation of gene expression data by Ramon Viñas, Helena Andrés-Terré, Pietro Liò, Kevin Bryson
  
• NASA SMD AI Workshop Report by SMD Artificial Intelligence (AI) Initiative
  

DNAStack COVID19 SRA Data

Tutorials

• Viral lineage assignment by Heather Ward
  AWS BatchAmazon EC2Amazon S3

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.
  

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
  

OpenCRAVAT

Tutorials

• Changing the OpenCRAVAT store url by Kyle Moad
  

Tools & Applications

• OpenCRAVAT by Karchinlab
  

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.
  

Reference data for HiFi human WGS

Tutorials

• PacBio WGS Variant Pipeline README by Pacific Biosciences of California, Inc
  

Tools & Applications

• Consolidated analysis with the PacBio WGS Variant Pipeline by Pacific Biosciences of California, Inc
  

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 PanGenomics Project

Publications

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

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
  

1KG-ONT-VIENNA panel

Publications

• Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project by Siegfried Schloissnig, Samarendra Pani, Bernardo Rodriguez-Martin, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Sarah Hunt, Tobias Rausch, Tobias Marschall, Jan O Korbel
  

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)