Showing 414 open source projects for "open-lates"

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  • 1

    iCAS - An Illumina Clone Assembly System

    An Illumina clone assembly system using SOAPdenovo and ABySS

    Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting...
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  • 2
    Generic Model Organism Database Project
    GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
    Downloads: 4 This Week
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  • 3
    Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
    Downloads: 7 This Week
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  • 4

    ENLY

    Bioinformatic tool to improve draft genome assemblies by closing gaps

    Downloads: 0 This Week
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  • 5
    NGS-TOOLBOX

    NGS-TOOLBOX

    Handy tools to process/analyze next generation sequencing (NGS) data

    The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication...
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  • 6

    czplib

    Chaolin Zhang's Perl Library

    Chaolin Zhang's Bioinformatic Perl Library
    Downloads: 14 This Week
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  • 7
    AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
    Downloads: 0 This Week
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  • 8

    mCarts

    A hidden Markov model to predict clustered RNA motif sites

    Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large...
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  • 9
    vcftools
    A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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    Downloads: 55 This Week
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  • 10

    bsclient

    An interactive FTP-like command-line BaseSpace download client

    bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient
    Downloads: 0 This Week
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  • 11

    SPA

    SPA: a short peptide assembler for metagenomic data

    The metagenomic paradigm offers the opportunity to study protein families, and therefore the metabolic and functional potential, of the constituent microbes in a community. A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short...
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  • 12
    The Protein Similarity Network

    The Protein Similarity Network

    Human protein similarity network used to predict drug safety.

    This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do...
    Downloads: 0 This Week
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  • 13
    EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.
    Downloads: 0 This Week
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  • 14

    BIRAP

    Bacterial Intergenic Region Analysis Pipeline

    BIRAP (Bacterial Intergenic Region Analysis Pipeline) is an open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics, compares it with existing in silico annotation and helps validate annotation, identify novel protein coding regions, putative non-coding RNA as well as help correct er-rors in the existing annotation. The pipeline requires “pileup” output...
    Downloads: 0 This Week
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  • 15
    Shoal

    Shoal

    A lot of fish in a shoal, in a gigantic scientific ocean.

    Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project...
    Downloads: 0 This Week
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  • 16
    SNiPlay
    SNiPlay is a web-based pipeline and database for SNP analysis and management
    Downloads: 0 This Week
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  • 17
    CARE2X - Integrated Hospital Info System
    Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab
    Downloads: 9 This Week
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  • 18

    iTagPlot

    A computation and interactive visualization of tag density

    iTagPlot is a computation and interactive visualization of tag density distribution for next generation sequencing data.
    Downloads: 1 This Week
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  • 19

    iMir

    Integrated pipeline for HT miRNA-Seq data analysis

    ... pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs.
    Downloads: 0 This Week
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  • 20

    CIMS

    Crosslinking induced mutation site analysis

    This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data. References: Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. Zhang,C.†, Darnell, R.B.† 2011....
    Downloads: 0 This Week
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  • 21
    The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
    Downloads: 1 This Week
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  • 22

    AMOS

    AMOS is a collection of tools for genome assembly

    AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
    Downloads: 8 This Week
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  • 23

    fastq2vcf

    WES analysis pipeline

    fasq2vcf is a program that generates an analysis pipeline for Whole Exome Sequencing (WES) projects. It takes the raw reads through to variant calling and annotation.
    Downloads: 0 This Week
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  • 24
    SimpleMap

    SimpleMap

    A tool to streamline high density genetic linkage group constrcution

    Downloads: 0 This Week
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  • 25
    Pipeline Builder for NGS tools

    Pipeline Builder for NGS tools

    Scripting tool for automatize and managing complex NGS analysis

    Handling with NGS tool configuration files is a real challenge for modern biologists and biotechnologist. To increase productivity, specificity and enhance the data processing, this tool provides a collection of commands already structured, leading the user in building the correct pipeline for the data he has to analyse. Pipeline Builder is a scripting tool for managing complex NGS analysis pipelines. It helps the user in composing NGS tool commands and composing his own analysis...
    Downloads: 0 This Week
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