Tools   Select Another Resource Report Type

http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/edgebio

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider.

Proper citation: EdgeBio (RRID:SCR_000183) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/genomics-services-lab

A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.

Proper citation: HudsonAlpha Genomics Services Lab (RRID:SCR_000353) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/pindel/0.2.4/

Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Pindel (RRID:SCR_000560) Copy   

•   Source: SciCrunch Registry

http://paleogenomics.irmacs.sfu.ca/FPSAC/

Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Proper citation: FPSAC (RRID:SCR_000555) Copy   

•   Source: SciCrunch Registry

http://genome.crg.es/software/gfftools/GFF2PS.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy   

•   Source: SciCrunch Registry

http://pringlelab.stanford.edu/projects.html

Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.

Proper citation: Fulcrum (RRID:SCR_005523) Copy   

•   Source: SciCrunch Registry

http://diprogb.fli-leibniz.de/

Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand.

Proper citation: DiProGB (RRID:SCR_005651) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/bismark/

Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step.

Proper citation: Bismark (RRID:SCR_005604) Copy   

•   Source: SciCrunch Registry

http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) Copy   

•   Source: SciCrunch Registry

http://genomefoundation.org/index.php/Main_Page

The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project

Proper citation: Genome Research Foundation (RRID:SCR_006056) Copy   

•   Source: SciCrunch Registry

http://pathogenseq.lshtm.ac.uk/estmoi

A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt).

Proper citation: estMOI (RRID:SCR_006192) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/HuREF/?SsId=78

The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies.

Proper citation: Human Reference Genetic Material Repository (RRID:SCR_004693) Copy   

•   Source: SciCrunch Registry

http://zgc.nci.nih.gov/

Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).

Proper citation: Zebrafish Gene Collection (RRID:SCR_007054) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/D_rerio/zmp/

Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue.

Proper citation: ZMP (RRID:SCR_006161) Copy   

•   Source: SciCrunch Registry

http://www.mousephenotype.org/

Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.

Proper citation: International Mouse Phenotyping Consortium (IMPC) (RRID:SCR_006158) Copy   

•   Source: SciCrunch Registry

https://github.com/HMPNK/CSA2.6

Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.

Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy   

•   Source: SciCrunch Registry

https://github.com/shendurelab/LACHESIS

Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.

Proper citation: LACHESIS (RRID:SCR_017644) Copy   

•   Source: SciCrunch Registry