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  1. github.com › ablab › spadesGitHub - ablab/spades: SPAdes Genome Assembler

    SPAdes package contains assembly pipelines for isolated and single-cell bacterial, as well as metagenomic and transcriptomic data. Additional modes allow to discover bacterial plasmids and RNA viruses, as well as perform HMM-guided assembly.

  2. ablab.github.io › spades › indexSPAdes Assembly Toolkit

    SPAdes package provides pipelines for DNA assembly of isolates and single-cell bacteria, as well as of metagenomic and transcriptomic data. Additional modes allow to recover bacterial plasmids and RNA viruses, perform HMM-guided assembly and more.

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  4. gensoft.pasteur.fr › docs › SPAdesSPAdes 3.13.1 Manual - Institut Pasteur

    SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.14.0 was released under GPLv2 on December 27, 2019 and can be downloaded from http://cab.spbu.ru/software/spades/. Supported data types.

  5. www.ncbi.nlm.nih.gov › pmc › articlesSPAdes: A New Genome Assembly Algorithm and Its Applications to...

    SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

  6. bioinformaticsworkbook.org › dataAnalysis › GenomeAssemblyIntroduction to SPAdes genome assembler - Bioinformatics Workbook

    SPAdes Genome paper 2012. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). SPAdes is a very memory intensive program. In multithreaded mode (-t 16), you will want at least 500 Gigabytes if not 1000 Gigabytes of RAM. How to run SPAdes. SPAdes parameter considerations. 1 2 3 4 5 6 7.

  7. medium.com › @BThors › using-spades-for-genome-assembly-a-step-by-step-guide-825Using SPAdes for Genome Assembly: A Step-by-Step Guide

    28 de dic. de 2022 · SPAdes (St. Petersburg genome assembler) is a popular open-source assembly tool for genome reconstruction from DNA sequencing reads. This article intents to demonstrate how to use SPAdes for...

  8. galaxy-au-training.github.io › tutorials › modulesGenome assembly - Galaxy Australia Training - GitHub Pages

    Spades is one of a number of de novo assemblers that use short read sets as input (e.g. Illumina Reads), and the assembly method is based on de Bruijn graphs. For information about Spades see this link. New to Galaxy? First try the introduction and then learn some key tasks. The data.

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