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http://dctd.cancer.gov/

Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine

Proper citation: DCTD (RRID:SCR_004196) Copy   

•   Source: SciCrunch Registry

http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.

Proper citation: IMG System (RRID:SCR_002965) Copy   

•   Source: SciCrunch Registry

http://www.portugene.com/SPInDel/SPInDel_webworkbench.html

A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.

Proper citation: SPInDel (RRID:SCR_004509) Copy   

•   Source: SciCrunch Registry

http://www.jainlab.org/downloads.html

Automatic software program for microarray image quantification.

Proper citation: UCSF Spot (RRID:SCR_002985) Copy   

•   Source: SciCrunch Registry

http://www.acmg.net

An organization composed of biochemical, clinical, cytogenetic, medical and molecular geneticists, genetic counselors and other health care professionals committed to the practice of medical genetics to Improve Health Through Medical Genetics. The American College of Medical Genetics and Genomics will: * Define and promote excellence in the practice of medical genetics and genomics in the integration of translational research into practice; * Promote and provide medical genetics and genomics education; * Increase access to medical genetics and genomics services and integrate them into patient care; * Advocate for and represent providers of medical genetics and genomics services and their patients; and * Maintain structure and integrity of ACMG and its value to members and the public.

Proper citation: American College of Medical Genetics and Genomics (RRID:SCR_005769) Copy   

•   Source: SciCrunch Registry

http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

•   Source: SciCrunch Registry

http://www.orpha.net/

European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.

Proper citation: Orphanet (RRID:SCR_006628) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/epigenomix.html

Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Proper citation: epigenomix (RRID:SCR_006407) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPaligner/soap2 (RRID:SCR_005503) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

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

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

https://omictools.com/tiltpicker-tool

Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing.

Proper citation: TiltPicker (RRID:SCR_016674) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://chlorobox.mpimp-golm.mpg.de/geseq.html

Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

Proper citation: GeSeq (RRID:SCR_017336) Copy   

•   Source: SciCrunch Registry

http://www.genome.gov/27549169

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV

Proper citation: NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) Copy   

•   Source: SciCrunch Registry