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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
http://www.biogazelle.com/qbaseplus
Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.
Proper citation: qBasePLUS (RRID:SCR_003370) Copy
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
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
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
http://www.bioinfor.com/zoom/general/overview.html
Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
Proper citation: ZOOM (RRID:SCR_002175) Copy
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
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
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
http://metagenomics.atc.tcs.com/SPHINX/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPHINX (RRID:SCR_000534) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: wANNOVAR (RRID:SCR_000565) Copy
A platform and application suite for bringing together omics and clinical data.
Proper citation: Syapse (RRID:SCR_012023) Copy
A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.
Proper citation: iOMICS (RRID:SCR_000239) Copy
A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing.
Proper citation: CloVR (RRID:SCR_005290) Copy
Open Source laboratory information management systems.
Proper citation: BIKA (RRID:SCR_011828) Copy
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
Commercial software company offering on-demand cloud, hybrid hosting, hosted private cloud, and dedicated infrastructure for complex needs.
Proper citation: GoGrid (RRID:SCR_013204) Copy
Service that retrieves disease relevant information from Twitter tweets and shows current hotspots of disease outbreaks on an interactive map. It is an ontology-driven system for detecting global health events
Proper citation: BioCaster (RRID:SCR_011869) Copy
Open source software for building AWS-compatible private and hybrid clouds for IT organizations in enterprises and technology businesses.
Proper citation: Eucalyptus (RRID:SCR_011872) Copy
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
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