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https://software.broadinstitute.org/gatk/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.

Proper citation: IndelGenotyper (RRID:SCR_016663) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/biotools/sequenza/

Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

Proper citation: Sequenza (RRID:SCR_016662) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances.

Proper citation: Supernova assembler (RRID:SCR_016756) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

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

Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

Proper citation: Rsubread (RRID:SCR_016945) Copy   

•   Source: SciCrunch Registry

https://github.com/schatzlab/genomescope

Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.

Proper citation: GenomeScope (RRID:SCR_017014) Copy   

•   Source: SciCrunch Registry

https://omicssimla.sourceforge.io

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy   

•   Source: SciCrunch Registry

https://github.com/PGB-LIV/VAPPER

Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.

Proper citation: VAPPER (RRID:SCR_016993) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

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

Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.

Proper citation: rnaSPAdes (RRID:SCR_016992) Copy   

•   Source: SciCrunch Registry

https://proteomics.cancer.gov/programs/cptac

Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies.

Proper citation: CPTAC (RRID:SCR_017135) Copy   

•   Source: SciCrunch Registry

https://www.trophoblast.cam.ac.uk/Resources/BioInformatics

Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training.

Proper citation: University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/shovill

Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.

Proper citation: shovill (RRID:SCR_017077) Copy   

•   Source: SciCrunch Registry

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

Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.

Proper citation: Goseq (RRID:SCR_017052) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/peddy

Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.

Proper citation: peddy (RRID:SCR_017287) Copy   

•   Source: SciCrunch Registry

https://github.com/ndierckx/NOVOPlasty

Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.

Proper citation: NOVOPlasty (RRID:SCR_017335) Copy   

•   Source: SciCrunch Registry

https://github.com/Sethupathy-Lab/miRquant

Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.

Proper citation: miRquant (RRID:SCR_017261) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/cgal/

Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.

Proper citation: Computing Genome Assembly Likelihoods (RRID:SCR_017624) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/batch_data.shtml

Software tool to access various mouse genome information in batch format. Batch data and analysis tools.

Proper citation: Batch Data and Analysis Tool (RRID:SCR_017515) Copy   

•   Source: SciCrunch Registry