Tools   Select Another Resource Report Type

http://primerdigital.com/fastpcr.html

Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching.

Proper citation: FastPCR (RRID:SCR_003155) Copy   

•   Source: SciCrunch Registry

http://cistrome.org/finder

Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.

Proper citation: CistromeFinder (RRID:SCR_005405) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

http://www.biopieces.org

A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).

Proper citation: Biopieces (RRID:SCR_005783) Copy   

•   Source: SciCrunch Registry

http://www.leicabiosystems.com/index.php?id=9161

A high performance, intuitive client viewer with integrated reporting functionality that can be used as a standalone viewer for accessing slides locally, or connected to Digital Image Hub for remote review.

Proper citation: Slidepath (RRID:SCR_005597) Copy   

•   Source: SciCrunch Registry

http://www.geospiza.com/Products/finchtv.shtml

Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FinchTV (RRID:SCR_005584) Copy   

•   Source: SciCrunch Registry

http://www.geneious.com/features/microsatellite-analysis

Free plugin that imports ABI fragment analysis ?les and allows you to visualize traces, ?t ladders, call peaks, predict bins, display alleles in a tabular format and export your data.

Proper citation: Geneious Microsatellite Plugin (RRID:SCR_005466) Copy   

•   Source: SciCrunch Registry

https://github.com/AdmiralenOla/Scoary

Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait.

Proper citation: Scoary (RRID:SCR_021087) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/clc-plugin/duplicate-reads-removal-plugin/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.

Proper citation: Duplicate reads removal (RRID:SCR_000231) Copy   

•   Source: SciCrunch Registry

http://www.lab7.io/

Software to address all aspects of Next Generation Sequencing data workflow.

Proper citation: Lab7 (RRID:SCR_001210) Copy   

•   Source: SciCrunch Registry

http://www.omixon.com/hla/

An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.

Proper citation: Omixon Target HLA Typing (RRID:SCR_001206) Copy   

•   Source: SciCrunch Registry

http://www.goldenhelix.com/SNP_Variation/SNP_Analysis_Package/index.html

SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.

Proper citation: SNP and Variation Suite SNP Analysis (RRID:SCR_001285) Copy   

•   Source: SciCrunch Registry

http://www.vectorfriends.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.

Proper citation: VectorFriends (RRID:SCR_001230) Copy   

•   Source: SciCrunch Registry

http://www.spiralgenetics.com/products/

Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid).

Proper citation: Anchored Assembly (RRID:SCR_001188) Copy   

•   Source: SciCrunch Registry

https://www.integromics.com/omicsoffice-for-ngs/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy   

•   Source: SciCrunch Registry

https://github.com/epigenomics/methylmaps

A data analysis pipeline for the Methyl-MAPS method.

Proper citation: Methyl-Analyzer (RRID:SCR_000318) Copy   

•   Source: SciCrunch Registry

https://www.infoquant.com/cghfusion

Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.

Proper citation: CGH Fusion (RRID:SCR_000295) Copy   

•   Source: SciCrunch Registry

https://github.com/hmsiccbl/screensaver

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays.

Proper citation: Screensaver (RRID:SCR_000297) Copy   

•   Source: SciCrunch Registry

http://anya.igsb.anl.gov/Geneways/GeneWays.html

System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

Proper citation: GeneWays (RRID:SCR_000572) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry