Search Results for "open source assembly software source code"

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Showing 13 open source projects for "open source assembly software source code"

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  • 1
    LP CSIC/UAB Apps and Code

    LP CSIC/UAB Apps and Code

    Software and Code from Laboratori de Proteòmica CSIC/UAB

    Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat )
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  • 2
    Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.
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  • 3

    ISVASE

    identification of sequence variant associated with splicing event

    To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data....
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  • 4

    RGAAT

    Reference based genome assembly and annotation for new genome

    This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).
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  • 5
    RErun

    RErun

    Create virtual DNA/RNA agarose gels

    RERun is a software tool for creating virtual agarose electrophoresis gels of nucleic acid fragments (restriction digests, PCR amplicons, etc). It is written in Perl and developed on Linux, although it can be made to run on Windows with some work (undocumented).
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  • 6
    allink

    allink

    Software for data analysis, image processing, simulations, solver.

    Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the...
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  • 7

    Assembly of mixed genomes

    Scripts used to assemble and deconvolute mixed mitochondrial genomes.

    Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424.
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  • 8
    The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.
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  • 9
    Disco (DIStribution of COnformations) is a software package for the estimation of solution conformations of organic molecules. It is rewritten form of NAMFIS method and can be used with the input files generated by Janocchio.
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  • 10
    DEPRECATED PROJECT! SolexaTools is becoming the SeqWare project (http://seqware.sourceforge.net) to better reflect its expanded sequencer support. Please go to this project page for code and documentation.
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  • 11
    DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV
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  • 12
    Bioinformatics tools and applications for the analysis of genomic sequence data.
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  • 13
    VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale.
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