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An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool
Proper citation: Taverna (RRID:SCR_004437) Copy
http://code.google.com/p/rna-star/
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
Proper citation: STAR (RRID:SCR_004463) Copy
http://www.sanger.ac.uk/resources/software/act/
A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
Proper citation: ACT: Artemis Comparison Tool (RRID:SCR_004507) Copy
http://compbio.cs.wayne.edu/software/squeezambler/
Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.
Proper citation: Squeezambler (RRID:SCR_004385) Copy
Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
Proper citation: SNiPer-HD (RRID:SCR_004383) Copy
http://sourceforge.net/projects/vanator-cvr/
A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.
Proper citation: Vanator (RRID:SCR_004370) Copy
http://www.csd.uwo.ca/~ilie/BOND/
Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.
Proper citation: Basic OligoNucleotide Design (RRID:SCR_004492) Copy
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy
A multiple-sample, technology-aware SNP and indel caller.
Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Proper citation: NuChart (RRID:SCR_004703) Copy
http://matsen.fhcrc.org/pplacer/
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
Proper citation: Pplacer (RRID:SCR_004737) Copy
Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.
Proper citation: TETRA (RRID:SCR_004573) Copy
A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.
Proper citation: QuickGO (RRID:SCR_004608) Copy
https://sites.google.com/a/lbl.gov/biopig/
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Proper citation: BioPig (RRID:SCR_004636) Copy
https://github.com/lmrodriguezr/nonpareil
Estimate average coverage and create Nonpareil curves for metagenomic datasets.
Proper citation: Nonpareil (RRID:SCR_004629) Copy
http://omics.informatics.indiana.edu/AbundanceBin/
An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.
Proper citation: AbundanceBin (RRID:SCR_004648) Copy
http://compbio.cs.sfu.ca/software-variation-hunter
A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.
Proper citation: VariationHunter (RRID:SCR_004865) Copy
http://www.ncbi.nlm.nih.gov/pubmed/
Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut.
Proper citation: PubMed (RRID:SCR_004846) Copy
http://www.cbcb.umd.edu/software/phymm/
Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.
Proper citation: Phymm and PhymmBL (RRID:SCR_004751) Copy
https://code.google.com/p/destruct/
A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.
Proper citation: deStruct (RRID:SCR_004747) Copy
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