Showing 9 open source projects for "soapdenovo"

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    Migrate to innovate with Red Hat Enterprise Linux on Azure

    Streamline your IT modernization journey with a holistic environment running Red Hat Enterprise Linux on Azure.

    With Red Hat Enterprise Linux on Azure, businesses can confidently modernize their IT environment, knowing they don’t have to compromise on security, scalability, reliability, and ease of management. Securely accelerate innovation and unlock a competitive edge with enterprise-grade modern cloud infrastructure.
  • Business Continuity Solutions | ConnectWise BCDR Icon
    Business Continuity Solutions | ConnectWise BCDR

    Build a foundation for data security and disaster recovery to fit your clients’ needs no matter the budget.

    Whether natural disaster, cyberattack, or plain-old human error, data can disappear in the blink of an eye. ConnectWise BCDR (formerly Recover) delivers reliable and secure backup and disaster recovery backed by powerful automation and a 24/7 NOC to get your clients back to work in minutes, not days.
  • 1
    GenSeed-HMM

    GenSeed-HMM

    Progressive assembly tool using DNA, protein or profile HMMs as seeds.

    ... seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.
    Downloads: 0 This Week
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  • 2

    Genobuntu

    Genobuntu Package for Next Generation Sequencing

    Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build ...
    Downloads: 6 This Week
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  • 3
    Downloads: 0 This Week
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  • 4

    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 in...
    Downloads: 0 This Week
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  • Run applications fast and securely in a fully managed environment Icon
    Run applications fast and securely in a fully managed environment

    Cloud Run is a fully-managed compute platform that lets you run your code in a container directly on top of Google's scalable infrastructure.

    Run frontend and backend services, batch jobs, deploy websites and applications, and queue processing workloads without the need to manage infrastructure.
  • 5
    SOAPdenovo2

    SOAPdenovo2

    Large-size genome de-novo assembler

    What's next of SOAPdenovo2: MEGAHIT is the formal successor of SOAPdenovo2 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph http://www.ncbi.nlm.nih.gov/pubmed/25609793 https://github.com/voutcn/megahit Latest Code on GitHub: https://github.com/aquaskyline/SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble...
    Downloads: 39 This Week
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  • 6
    SOAPdenovo-Trans

    SOAPdenovo-Trans

    A de novo transcriptome assembler.

    Latest Codes on GitHub: https://github.com/aquaskyline/SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. The assembler provides a more comprehensive way to construct the full-length transcript sets compare to SOAPdenovo2.
    Downloads: 1 This Week
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  • 7
    mitoMaker

    mitoMaker

    mitoMaker - a mitochondria assembly and annotation script

    mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target...
    Downloads: 0 This Week
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  • 8

    mitoMaker

    mitoMaker - a mitochondria pipeline wrapper script

    ... started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). If a feature was missing, or it hasn't circularized, try and assemble again with different assembler parameters (mainly k-mer). Rinse and repeat until the best build is found.
    Downloads: 1 This Week
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  • 9

    PASHA: Parallelized Short Read Assembly

    One of the fastest parallel short read assemblers for large genomes.

    ... compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU. For the human genome, PASHA achieves competitive assembly quality with ABySS and is able to complete the assembly in about 21 hours, which is about 2.38× faster than ABySS on the same hardware configurations.
    Downloads: 0 This Week
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  • Android Device Management for tablets, kiosks, POS, rugged devices, and more Icon
    Android Device Management for tablets, kiosks, POS, rugged devices, and more

    For single-use devices that are vertical specific like POS, Kiosk, ATM, Digital Signage, etc.

    Esper is the industry's most powerful and comprehensive solution for single-purpose Android Enterprise devices such as kiosks, tablets, mPoS, digital signage, and more. It offers powerful, intuitive features to configure, deploy, and manage the your devices. It empowers control over the enterprise Android device lifecycle, including hardware, firmware, app development, monitoring, and remote remediation. Esper is the first solution to combine custom OS, enhanced firmware, a complete DevOps toolchain, and endpoint detection and response. Esper's full-stack admin suite goes beyond a regular MDM with unprecedented support for device management, remote control, and real-time OTA updates. It's the only single-dashboard suite for remote device diagnostics, advanced telemetry and debugging.
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