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http://sourceforge.net/projects/probeselect/
Software for selecting probes in heterogenous transcriptional sets.
Proper citation: ProbeSelect (RRID:SCR_012965) Copy
http://sourceforge.net/projects/seqgenomebrowse/
Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data.
Proper citation: SeqGenome Browser (RRID:SCR_012970) Copy
http://sourceforge.net/projects/mirdp/
A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
Proper citation: miRDeep-P (RRID:SCR_013026) Copy
http://sourceforge.net/projects/quicktsaf/
Tool that compresses and decompresses fastq files.
Proper citation: KungFq (RRID:SCR_012979) Copy
http://sourceforge.net/projects/ncproseq/
Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.
Proper citation: ncPRO-seq (RRID:SCR_013031) Copy
http://sourceforge.net/projects/vcf2msat/
A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files.
Proper citation: vcf2MSAT (RRID:SCR_013034) Copy
http://sourceforge.net/projects/fishingcnv/
A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.
Proper citation: FishingCNV (RRID:SCR_013038) Copy
http://sourceforge.net/projects/msaprobs/
An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.
Proper citation: MSAProbs (RRID:SCR_012982) Copy
http://sourceforge.net/projects/qcreads/
Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.
Proper citation: QcReads (RRID:SCR_013002) Copy
http://sourceforge.net/projects/hector454/
A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.
Proper citation: HECTOR (RRID:SCR_013007) Copy
http://sourceforge.net/projects/mirdeepstar/
An integrated application software tool for miRNA identification from RNA sequencing data.
Proper citation: miRDeep* (RRID:SCR_012960) Copy
http://sourceforge.net/projects/amos/
A collection of tools and class interfaces for the assembly of DNA reads.
Proper citation: AMOS (RRID:SCR_013067) Copy
http://sourceforge.net/projects/contrail-bio/
A Hadoop based genome assembler for assembling large genomes in the clouds.
Proper citation: Contrail (RRID:SCR_013066) Copy
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
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
A complete software system used to store and analyze gene expression data.
Proper citation: GEOSS (RRID:SCR_003401) Copy
http://sourceforge.net/projects/amplicon/
Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
Proper citation: Amplicon (RRID:SCR_003294) Copy
http://purl.bioontology.org/ontology/FB-SP
The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy
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
http://cliiq.sourceforge.net/Home
An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.
Proper citation: CLIIQ (RRID:SCR_009972) Copy
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