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https://www.4dnucleome.org

Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.

Proper citation: 4D Nucleome (RRID:SCR_016925) Copy   

•   Source: SciCrunch Registry

https://github.com/asdcid/Gene-conservation-informed-contig-alignment

Software tool for separation haplotigs from genome assembly. Method to separate haplotigs based on sequence similarity.

Proper citation: Gene-conservation-informed-contig-alignment (RRID:SCR_017617) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-Qingdao/TGS-GapCloser

Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.

Proper citation: TGS-GapCloser (RRID:SCR_017633) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry

https://github.com/AnacletoLAB/parSMURF

Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants.

Proper citation: parSMURF (RRID:SCR_017560) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/ATACseqMappingPipeline

Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them.

Proper citation: ATACseqMappingPipeline (RRID:SCR_017558) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

http://cccb.dfci.harvard.edu

Core facility that provides the following services: Microarray and other genomic data analysis, MiSeq. The Center provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research. The CCCB has three primary elements. * The CCCB sequencing facility offers a wide range of services to assist in the design and execution of next-generation sequencing projects. Utilizing the Illumina (Solexa) sequencing technology, they currently support a number of applications inlcuding ChIP-Seq, RNA-Seq, whole genome, whole exome, and targeted re-sequencing. * The analytical services and support platform aims to provide state-of-the-art assistance in the collection, management, analysis, and interpretation of large-scale data with a focus on data generated using ''''omic technologies. In addition, they offer software, services, and training designed to assist investigators in advancing their research. * The CCCB research program is focused on development of new methods for improving analysis and interpretation of genomic data through integration of diverse data types with the goal of creating open-source software tools to be made freely-available to the research community.

Proper citation: DFCI Center for Cancer Computational Biology (RRID:SCR_012688) Copy   

•   Source: SciCrunch Registry

https://www.integromics.com/omicsoffice-for-ngs/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy   

•   Source: SciCrunch Registry

http://mus.well.ox.ac.uk/mouse/INBREDS/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.

Proper citation: Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/node/549

Genomic data set on Type 2 Diabetes in African-Americans derived via admixture mapping, a method for genome-wide association analysis based on admixture-generated linkage disequilibrium. This collaborative group has identified 1,478 African Americans with Type 2 Diabetes (T2D) from the Jackson Heart Study and Multiethnic Cohort Study, as well as 498 controls from the Jackson Heart Study who are normoglycemic despite high body mass index and older age. All samples were genotyped (using the Illumina BeadLab platform) for 1,291 polymorphic markers chosen to be extremely different in frequency between west Africans and European Americans. Evidence for association to diabetes at each marker as reported by the ANCESTRYMAP software are reported in the downloadable table. They calculate that this study has statistical power to detect loci where African or European ancestry on average confers multiplicative increased risk of 1.35-fold or more. The fact that they did not detect a statistically significant signal of association in the scan suggests that any genetic risk factors for T2D do not confer different risks due to ancestry that differ by this factor. The genome scan results are publicly available (Excel file) prior to publication so that researchers interested in the genetics of T2D can use the results of the scan to prioritize follow-up of any regions of interest.

Proper citation: A Whole Genome Admixture Scan for Type 2 Diabetes in African Americans (RRID:SCR_006984) Copy   

•   Source: SciCrunch Registry

http://eyebrowse.cit.nih.gov/

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Proper citation: EyeBrowse (RRID:SCR_008000) Copy   

•   Source: SciCrunch Registry

http://www.hgvs.org/dblist/dblist.html

A list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don''''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Students

Proper citation: Human Genome Variation Society: Databases and Other Tools (RRID:SCR_006876) Copy   

•   Source: SciCrunch Registry

http://www.einstein.yu.edu/departments/genetics/resources/molecular-cytogenetics-core.aspx

Core provides tools for preparation of human and murine samples suitable for molecular genetic and cytogenetic analysis of entire genome. These tools include establishment of EBV transformed cell lines; isolation of DNA and mRNA from variety of tissue culture samples as well as primary biopsies; preparation of metaphase chromosomes suitable for fluorescence in situ hybridization (FISH) and Spectral Karyotyping (SKY) or whole chromosome paints for human and mouse genome. Core personnel is trained to hybridize commercial probes and to designed locus specific probes for regions of interest to investigators. All probes are custom designed and in house generated.

Proper citation: Albert Einstein College of Medicine Molecular Cytogenetics Core Facility (RRID:SCR_017815) Copy   

•   Source: SciCrunch Registry

http://htbc.stanford.edu

Core provides fully automated high throughput screening (HTS) of Compound Libraries (130,000+ compounds) for both enzyme/protein-based assays and cell-based assays, using Caliper Life Sciences Staccato system;Genomic siRNA screening with siARRAY whole human genome siRNA library from Dharmacon targeting 21,000 genes, using Agilent Bravo system;High-Content Screening using ImageXpress Micro automated fluorescent microscope with live cell, bright field, phase contrast and integrated plate handling with Thermo Catalyst CRS, and image analysis using MetaXpress software;High Throughput Molecular Biology reagents and services, including access to cDNA libraries (Human ORFeome collection, 15,000 genes) and 96 and 384-well bead clean-ups and PCR setup (Biomek FX and Agilent Bravo), and other automation steps in collaboration with SFGF;High-throughput assay development assistance with cell culture, experiment design, robotic programming and Standard Operating Procedure drafting;Screening data analysis assistance with protocols, hit determination and structure activity analyses using MDL chemical database ISIS/HOST, Plate Manager, Assay Explorer and Report Manager. Use of microplate reader detection systems, including Tecan Infinite M1000 and Infinite M1000 PRO and Molecular Devices Analyst GT for fluorescence; fluorescence polarization; time-resolved fluorescence; absorbance and luminescence (with injectors and AlphaScreen); and Flexstation II 384, for kinetic fluorescence reads to measure calcium mobilization and ion channels.Use of liquid-handling robots, including Sciclone ALH3000 (96- and 384-well pipetting), Agilent Bravo (96- and 384-well pipetting), Velocity11 VPrep (96-well pipetting), Bio-Tek plate washers/dispensers, Matrix Wellmate and Titertek/Labsystems Multidrop microplate dispensers, and Velocity11 PlateLoc plate heat sealer;Training for most of these services.

Proper citation: Stanford University School of Medicine High Throughput Bioscience Center Core Facility (RRID:SCR_017794) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/genome-technology-center

Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results.

Proper citation: New York University School of Medicine Langone Health Genome Technology Center Core Facility (RRID:SCR_017929) Copy   

•   Source: SciCrunch Registry

http://mousebiology.org

Core located on campus of UC Davis, providing fully customized support for scientific research using genetically altered mice. Provides access to develop, plan, execute, and analyze research project involving genetically-altered mice. Provides description of project, including alternative approaches, accurate timelines, and cost estimates.Provides regular and informative communication throughout project, including email updates on completion of each milestone. Project progress can be followed at each stage by viewing detailed information anytime by accessing our online and secure project tracking system (PTS) available 24 hours a day.

Proper citation: University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility (RRID:SCR_017851) Copy   

•   Source: SciCrunch Registry

http://hihg.med.miami.edu/cgt/gene-expression

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip.

Proper citation: University of Miami Miller School of Medicine Gene Expression Core Facility (RRID:SCR_017825) Copy   

•   Source: SciCrunch Registry

https://github.com/adigenova/fast-sg

Algorithm for alignment-free scaffolding graph construction from short or long reads. It allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines.

Proper citation: Fast-SG (RRID:SCR_015934) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

•   Source: SciCrunch Registry