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http://cushaw2.sourceforge.net/homepage.htm#latest

Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome.

Proper citation: CUSHAW (RRID:SCR_005479) Copy   

•   Source: SciCrunch Registry
  

http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry
  

http://samtools.sourceforge.net/tview.shtml

Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.

Proper citation: SAMtools Text Alignment Viewer (RRID:SCR_005611) Copy   

•   Source: SciCrunch Registry
  

http://manatee.sourceforge.net/

Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris

Proper citation: Manatee (RRID:SCR_005685) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cancergrid-tma/

A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.

Proper citation: cancergrid-tma (RRID:SCR_005595) Copy   

•   Source: SciCrunch Registry
  

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dna-bison/

Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.

Proper citation: dna-bison (RRID:SCR_005913) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cohcap/

An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

Proper citation: COHCAP (RRID:SCR_006499) Copy   

•   Source: SciCrunch Registry
  

http://theswo.sourceforge.net

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

Proper citation: Software Ontology (RRID:SCR_003493) Copy   

•   Source: SciCrunch Registry
  

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry
  

http://jmol.sourceforge.net/

An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.

Proper citation: Jmol (RRID:SCR_003796) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/insertionmapper/

A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Proper citation: InsertionMapper (RRID:SCR_004163) Copy   

•   Source: SciCrunch Registry
  

http://cb-commander.sourceforge.net/pmwiki.php

A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.

Proper citation: CB-Commander (RRID:SCR_004237) Copy   

•   Source: SciCrunch Registry
  

http://rubioseq.sourceforge.net/

Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

Proper citation: RUbioSeq (RRID:SCR_002508) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/b-o-s-s/

Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mipe/

A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.

Proper citation: MIPE (RRID:SCR_003065) Copy   

•   Source: SciCrunch Registry
  

http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry
  

http://sobekrepository.org/

Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

Proper citation: SobekCM (RRID:SCR_003225) Copy   

•   Source: SciCrunch Registry
  

http://www.metabolomics-msi.org

Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.

Proper citation: Metabolomics Standards Initiative (RRID:SCR_003246) Copy   

•   Source: SciCrunch Registry
  

http://splicq.sourceforge.net/

A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.

Proper citation: SpliCQ (RRID:SCR_003266) Copy   

•   Source: SciCrunch Registry