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https://www.gencodegenes.org

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

Proper citation: GENCODE (RRID:SCR_014966) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/Sniffles

Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.

Proper citation: Sniffles (RRID:SCR_017619) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/cgi-bin/hgLiftOver

Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.

Proper citation: liftOver (RRID:SCR_018160) 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://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry

https://github.com/greenelab/miQC

Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset.

Proper citation: miQC (RRID:SCR_022697) Copy   

•   Source: SciCrunch Registry

https://het.io/search/

Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.

Proper citation: Hetnet Connectivity Search (RRID:SCR_023630) Copy   

•   Source: SciCrunch Registry

https://reactome.org/

Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis.

Proper citation: Reactome Knowledgebase (RRID:SCR_023504) Copy   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/PhenStat.html

Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.

Proper citation: PhenStat (RRID:SCR_021317) Copy   

•   Source: SciCrunch Registry

https://my.locuszoom.org

Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

Proper citation: LocusZoom.org (RRID:SCR_021374) Copy   

•   Source: SciCrunch Registry

https://crispresso.pinellolab.partners.org/submission

Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso (RRID:SCR_021538) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/salsa

Software tool for scaffold long read assemblies with Hi-C data.

Proper citation: SALSA (RRID:SCR_022013) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/charade/svengine

Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats.

Proper citation: SVEngine (RRID:SCR_016235) Copy   

•   Source: SciCrunch Registry

http://www.repeatmasker.org/RepeatModeler/

Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RepeatModeler (RRID:SCR_015027) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/BioDepot-workflow-builder

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy   

•   Source: SciCrunch Registry

http://deweylab.biostat.wisc.edu/detonate/

Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.

Proper citation: DETONATE (RRID:SCR_017035) Copy   

•   Source: SciCrunch Registry

https://web.expasy.org/protparam/

Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.

Proper citation: ProtParam Tool (RRID:SCR_018087) Copy   

•   Source: SciCrunch Registry

https://cadd.gs.washington.edu/

Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.

Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy   

•   Source: SciCrunch Registry