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http://sourceforge.net/projects/phaccs/
Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
Proper citation: PHACCS (RRID:SCR_001232) Copy
Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.
Proper citation: QUAST (RRID:SCR_001228) Copy
http://sourceforge.net/projects/kanalyze/
A Java toolkit designed to convert DNA and RNA sequences into k-mers.
Proper citation: KAnalyze (RRID:SCR_001323) Copy
https://sourceforge.net/p/obo/mailman/message/59165700/
A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.
Proper citation: Drosophila anatomy and development ontologies (RRID:SCR_001607) Copy
http://sourceforge.net/projects/baccontigeditor/
A simple sequence alignment editing tool, written in Java.
Proper citation: BACContigEditor (RRID:SCR_001617) Copy
http://sourceforge.net/projects/dnaclust/
Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.
Proper citation: DNACLUST (RRID:SCR_001771) Copy
http://biolemmatizer.sourceforge.net/
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Proper citation: BioLemmatizer (RRID:SCR_000117) Copy
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
http://sourceforge.net/projects/cnv/
Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
Proper citation: CNV Workshop (RRID:SCR_012635) Copy
http://sourceforge.net/p/krona/home/krona/
Software that allows hierarchical data to be explored with zoomable pie charts.
Proper citation: Krona (RRID:SCR_012785) Copy
http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar
Accurate error-correction of amplicon pyrosequences.
Proper citation: Acacia (RRID:SCR_012896) Copy
http://sourceforge.net/projects/ibdld/
A C++ software program for multipoint IBD estimation based on high density SNP genotype data.
Proper citation: IBDLD (RRID:SCR_013043) Copy
http://sourceforge.net/projects/solsnp/
A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.
Proper citation: SolSNP (RRID:SCR_013045) Copy
http://sourceforge.net/projects/tumorhats/
A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.
Proper citation: HATS (RRID:SCR_013044) Copy
http://sourceforge.net/projects/chipotle-perl/
A peak-finding algorithm used to analyze ChIP-chip microarray data.
Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy
http://trinityrnaseq.sourceforge.net/
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Proper citation: Trinity (RRID:SCR_013048) Copy
http://sourceforge.net/projects/ngspeanalysis/
A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.
Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy
http://sourceforge.net/projects/lofreq/
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
Proper citation: LoFreq (RRID:SCR_013054) Copy
http://sourceforge.net/projects/genecounter/
A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
Proper citation: GENE-counter (RRID:SCR_013056) Copy
http://sourceforge.net/projects/rnacompass/
A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.
Proper citation: RNA CoMPASS (RRID:SCR_013058) Copy
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