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Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms.
Proper citation: Johns Hopkins University School of Medicine Genetic Resources Core Facility (RRID:SCR_018669) Copy
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
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
https://einsteinmed.edu/research/shared-facilities/cores/53/epigenomics/
Part of Einstein Center for Epigenomics and Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and number of assays to study the genome/epigenome. Data analytical services are provided by Computational Genomics Facility.
Proper citation: Albert Einstein College of Medicine Epigenomics Shared Core Facility (RRID:SCR_023284) Copy
https://github.com/huangnengCSU/compleasm
Software genome completeness evaluation tool based on miniprot.
Proper citation: compleasm (RRID:SCR_026370) Copy
https://github.com/YongyiLuo98/BVSim
Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum.
Proper citation: BVSim (RRID:SCR_026926) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/SlideTags_Pipeline/README
Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification.
Proper citation: SlideTags.wdl (RRID:SCR_027567) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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