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http://sourceforge.net/projects/fishingcnv/
A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data.
Proper citation: FishingCNV (RRID:SCR_013038) Copy
http://sourceforge.net/projects/msaprobs/
An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks.
Proper citation: MSAProbs (RRID:SCR_012982) Copy
http://sourceforge.net/projects/qcreads/
Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms.
Proper citation: QcReads (RRID:SCR_013002) Copy
http://sourceforge.net/projects/rdpframebot/
A frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline.
Proper citation: RDP FrameBot (RRID:SCR_013083) Copy
http://sourceforge.net/projects/hector454/
A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.
Proper citation: HECTOR (RRID:SCR_013007) Copy
http://sourceforge.net/projects/mirdeepstar/
An integrated application software tool for miRNA identification from RNA sequencing data.
Proper citation: miRDeep* (RRID:SCR_012960) Copy
http://sourceforge.net/projects/amos/
A collection of tools and class interfaces for the assembly of DNA reads.
Proper citation: AMOS (RRID:SCR_013067) Copy
http://sourceforge.net/projects/contrail-bio/
A Hadoop based genome assembler for assembling large genomes in the clouds.
Proper citation: Contrail (RRID:SCR_013066) Copy
http://easyfig.sourceforge.net/
A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).
Proper citation: Easyfig (RRID:SCR_013169) Copy
http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
http://sourceforge.net/projects/palfinder/
A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.
Proper citation: palfinder (RRID:SCR_013174) Copy
http://sourceforge.net/projects/samcomp/
A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
Proper citation: sam comp (RRID:SCR_013179) Copy
http://sourceforge.net/projects/heuraa/
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Proper citation: HeurAA (RRID:SCR_013212) Copy
http://sourceforge.net/projects/bisreadmapper/
Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.
Proper citation: bisReadMapper (RRID:SCR_013171) 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
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