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http://sourceforge.net/projects/taxoassignement/
Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy.
Proper citation: TaxoAssignement (RRID:SCR_006814) Copy
http://sourceforge.net/projects/celeragb/
Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.
Proper citation: Celera Genome Browser (RRID:SCR_013093) Copy
http://sourceforge.net/projects/socs/
Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.
Proper citation: SOCS (RRID:SCR_013223) Copy
http://sourceforge.net/projects/denovosolid/
Pipeline for small genome assembly using SOLiD sequencing technology.
Proper citation: DSP (RRID:SCR_013114) Copy
http://sourceforge.net/projects/tuxe/
Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.
Proper citation: Tuxedo (RRID:SCR_013194) Copy
http://seqtracs.sourceforge.net/
Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility.
Proper citation: SeqTRACS (RRID:SCR_013294) Copy
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
A scalable software pipeline for whole genome resequencing analysis.
Proper citation: Crossbow (RRID:SCR_013306) Copy
http://sourceforge.net/tracker/?group_id=76834&atid=835555
Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.
Proper citation: OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) Copy
http://sourceforge.net/p/mira-assembler/wiki/Home/
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Proper citation: MIRA (RRID:SCR_010731) Copy
http://sourceforge.net/projects/xdrawchem/
A drawing software application designed for drawing and analyzing chemical structures and reactions.
Proper citation: XDrawChem (RRID:SCR_010941) Copy
A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.
Proper citation: PPSEQ (RRID:SCR_010913) Copy
http://sourceforge.net/p/arpeggio/wiki/Home/
Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.
Proper citation: Arpeggio (RRID:SCR_010876) Copy
http://xmsanalyzer.sourceforge.net
A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.
Proper citation: xMSanalyzer (RRID:SCR_012144) Copy
http://sourceforge.net/projects/excavatortool/
A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
Proper citation: EXCAVATOR-tool (RRID:SCR_012766) Copy
http://sourceforge.net/projects/trowel-ec/
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Proper citation: Trowel (RRID:SCR_012890) Copy
http://sourceforge.net/projects/oncosts/
Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.
Proper citation: Onco-STS (RRID:SCR_012990) Copy
http://sourceforge.net/projects/nxgview/
A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.
Proper citation: NxGview (RRID:SCR_012994) Copy
http://sourceforge.net/projects/bamformatics/
Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.
Proper citation: Bamformatics (RRID:SCR_013041) Copy
http://sourceforge.net/projects/bsmapper/
Sequence mapper for bisulfite sequencing reads for DNA methylation studies.
Proper citation: BSmapper (RRID:SCR_012998) Copy
http://sourceforge.net/projects/mendelscan/
A software tool for prioritizing candidate variants in family-based studies of inherited disease.
Proper citation: MendelScan (RRID:SCR_013053) Copy
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