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http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2

A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage.

Proper citation: V-Phaser 2 (RRID:SCR_005212) Copy   

•   Source: SciCrunch Registry

http://rnaexpress.org/

Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.

Proper citation: RNA-eXpress (RRID:SCR_005167) Copy   

•   Source: SciCrunch Registry

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

Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Proper citation: SAMtools/BCFtools (RRID:SCR_005227) 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

https://github.com/lpantano/seqbuster

Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.

Proper citation: SeqBuster (RRID:SCR_009616) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

http://dna.engr.uconn.edu/?page_id=105

Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.

Proper citation: IsoEM (RRID:SCR_009993) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bitseq/

A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Proper citation: BitSeq (RRID:SCR_009904) Copy   

•   Source: SciCrunch Registry

http://beast.bio.ed.ac.uk/

A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Proper citation: BEAST (RRID:SCR_010228) Copy   

•   Source: SciCrunch Registry

http://weblogo.berkeley.edu

Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.

Proper citation: WEBLOGO (RRID:SCR_010236) Copy   

•   Source: SciCrunch Registry

http://www.genome.umd.edu/masurca.html

A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MaSuRCA (RRID:SCR_010691) Copy   

•   Source: SciCrunch Registry

http://pathema.jcvi.org/Pathema/index.html

Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource.

Proper citation: Pathema (RRID:SCR_010585) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.

Proper citation: ABySS (RRID:SCR_010709) Copy   

•   Source: SciCrunch Registry

http://icy.bioimageanalysis.org/

An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download.

Proper citation: icy (RRID:SCR_010587) Copy   

•   Source: SciCrunch Registry

http://www.geneious.com/

Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.

Proper citation: Geneious (RRID:SCR_010519) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/CNVer/

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.

Proper citation: CNVer (RRID:SCR_010820) Copy   

•   Source: SciCrunch Registry

http://www.popgen.dk/software/index.php/Relate

Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.

Proper citation: Relate (RRID:SCR_010794) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/modil/

Software for a novel method for finding medium sized indels from high throughput sequencing datasets.

Proper citation: MoDIL (RRID:SCR_010764) Copy   

•   Source: SciCrunch Registry