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A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
http://fureylab.web.unc.edu/software/fseq/
A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.
Proper citation: F-Seq (RRID:SCR_010880) Copy
Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
Proper citation: HOMER (RRID:SCR_010881) Copy
Database for microarray data storage, retrieval, analysis, and visualization.
Proper citation: UNC Microarray Database (RRID:SCR_010979) Copy
http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer
An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data.
Proper citation: ABySS-Explorer (RRID:SCR_010980) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Hawkeye
A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors.
Proper citation: Hawkeye (RRID:SCR_010982) Copy
http://www.raetschlab.org/suppl/palmapper
Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
Proper citation: PALMapper (RRID:SCR_011466) Copy
Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.
Proper citation: PiMS (RRID:SCR_011816) Copy
A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.
Proper citation: Annmap (RRID:SCR_011783) Copy
http://fgcz-bfabric.uzh.ch/bfabric/
An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis.
Proper citation: B-Fabric (RRID:SCR_011827) Copy
http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform.
Proper citation: Galaxy LIMS (RRID:SCR_011829) Copy
http://archimedes.cheme.cmu.edu/?q=gpublast
Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries.
Proper citation: GPU-BLAST (RRID:SCR_011820) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
A web-based tool used to search translated nucleotide databases using a translated nucleotide query.
Proper citation: TBLASTX (RRID:SCR_011823) Copy
An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more.
Proper citation: IGB (RRID:SCR_011792) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
http://pipmaker.bx.psu.edu/pipmaker/
PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Proper citation: PipMaker and MultiPipMaker (RRID:SCR_011806) Copy
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