Tools   Select Another Resource Report Type

http://sourceforge.net/projects/primerdesigner/

High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dranew/defuse

Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.

Proper citation: deFuse (RRID:SCR_003279) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CMO

An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

Proper citation: Clinical Measurement Ontology (RRID:SCR_003291) Copy   

•   Source: SciCrunch Registry

http://primerseq.sourceforge.net/

Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.

Proper citation: PrimerSeq (RRID:SCR_003295) Copy   

•   Source: SciCrunch Registry

https://github.com/gbook/nidb

Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.

Proper citation: NIDB - Neuroinformatics Database (RRID:SCR_002488) Copy   

•   Source: SciCrunch Registry

http://scralyze.sourceforge.net

A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.

Proper citation: SCRalyze (RRID:SCR_002542) Copy   

•   Source: SciCrunch Registry

http://andestools.sourceforge.net/

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Proper citation: ANDES (RRID:SCR_002791) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/glprobs/

Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.

Proper citation: GLProbs (RRID:SCR_002739) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bio-rainbow/

Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Proper citation: Rainbow (RRID:SCR_002724) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Proper citation: Bambus (RRID:SCR_005068) Copy   

•   Source: SciCrunch Registry

http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

Proper citation: G-BLASTN (RRID:SCR_005062) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cova/

A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype.

Proper citation: COVA (RRID:SCR_005175) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qure/

A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

Proper citation: QuRe (RRID:SCR_005209) Copy   

•   Source: SciCrunch Registry

http://unoseq.sourceforge.net/

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

Proper citation: UnoSeq (RRID:SCR_005116) Copy   

•   Source: SciCrunch Registry

http://orman.sourceforge.net/Home

A software tool for resolving multi-mappings within an RNA-Seq SAM file.

Proper citation: ORMAN (RRID:SCR_005188) Copy   

•   Source: SciCrunch Registry

http://seqant.genetics.emory.edu/

A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.

Proper citation: SeqAnt (RRID:SCR_005186) Copy   

•   Source: SciCrunch Registry

http://ergatis.sourceforge.net/

A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

Proper citation: Ergatis (RRID:SCR_005377) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

http://splitread.sourceforge.net/

Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.

Proper citation: SPLITREAD (RRID:SCR_005264) Copy   

•   Source: SciCrunch Registry