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Airam Rojas Zerpa
Airam Rojas Zerpa

SPAdes Manual: Installation and Running Guide for SPAdes Genome Assembler


How to Download and Use SPAdes Assembler




SPAdes - St. Petersburg genome assembler - is an assembly toolkit that contains various assembly pipelines for different types of sequencing data. It was originally developed for de novo assembly of bacterial and viral genomes from single-cell or isolate samples, but it has been extended to support metagenomic, plasmid, transcriptomic, and biosynthetic gene cluster assembly as well. SPAdes can also perform hybrid assembly using short reads (Illumina or IonTorrent) and long reads (PacBio, Oxford Nanopore, or Sanger). SPAdes is one of the most widely used assemblers in the field, and it has several advantages over other assemblers, such as:


  • It can handle complex repeat structures and large genome variations.



  • It can produce high-quality assemblies with low error rates and high gene completeness.



  • It can assemble genomes from low-coverage or unevenly distributed data.



  • It can assemble multiple genomes from mixed samples.



  • It can assemble novel sequences that are not present in reference genomes.



In this article, I will show you how to download and use SPAdes assembler for your own genome assembly projects. I will cover the following topics:




download spades assembler



  • How to download SPAdes binaries or source code for Linux or Mac.



  • How to verify your installation and run a self-test.



  • How to provide input data and command line options for different assembly pipelines.



  • How to evaluate the output files and statistics.



By the end of this article, you should be able to perform de novo genome assembly using SPAdes with confidence and ease. Let's begin!


Downloading SPAdes




The first step is to download SPAdes from its official website: . You can choose to download either the pre-compiled binaries or the source code, depending on your operating system and preference. The latest version of SPAdes is 3.15.5, which was released on July 14th, 2022 under GPLv2 license.


Downloading SPAdes binaries for Linux




If you are using a Linux system (64-bit only), you can download the pre-compiled binaries from the website. The file name is SPAdes-3.15.5-Linux.tar.gz. You can use the following command to download it:


wget


Alternatively, you can use a web browser to download it manually. After downloading, you need to extract the file using the following command:


tar -xzf SPAdes-3.15.5-Linux.tar.gz


This will create a folder named SPAdes-3.15.5-Linux, which contains the executable files and other resources for SPAdes.


Downloading SPAdes binaries for Mac




If you are using a Mac system (64-bit only), you can download the pre-compiled binaries from the website as well. The file name is SPAdes-3.15.5-Darwin.tar.gz. You can use the following command to download it:


How to download spades assembler for Linux


Download spades assembler binaries for Mac OS


Download and compile spades assembler source code


Verify spades assembler installation


Spades assembler input formats and options


Spades assembler command line usage and examples


Spades assembler output files and formats


Spades assembler performance and benchmarks


Spades assembler manual and support


Spades assembler citation and publications


Download spades assembler for metagenomic data sets


Download spades assembler for plasmid extraction and assembly


Download spades assembler for transcriptome assembly


Download spades assembler for biosynthetic gene cluster assembly


Download spades assembler for RNA viral data sets


Spades assembler pipeline overview and comparison


Spades assembler hybrid mode with PacBio, Nanopore or Sanger reads


Spades assembler HMM-guided mode with gene models


Spades assembler coronaSPAdes pipeline for coronavirus data sets


Spades assembler rnaviralSPAdes pipeline for RNA viral data sets


Spades assembler metaviralSPAdes pipeline for viral metagenomes


Spades assembler metaSPAdes pipeline for metagenomes


Spades assembler plasmidSPAdes pipeline for plasmids from WGS data sets


Spades assembler metaplasmidSPAdes pipeline for plasmids from metagenomes


Spades assembler rnaSPAdes pipeline for RNA-Seq data sets


Spades assembler biosyntheticSPAdes pipeline for biosynthetic gene clusters


Spades assembler GAGE-B data sets benchmark results and analysis


Spades assembler stand-alone binaries and tools description and usage


Spades assembler k-mer counting tool (spades-hammer)


Spades assembler k-mer coverage read filter tool (spades-bwa)


Spades assembler k-mer cardinality estimating tool (spades-kmercount)


Spades assembler graph construction tool (spades-core)


Spades assembler long read to graph alignment tool (spaligner)


Spades assembler hybridSPAdes aligner tool (hybrid_aligner)


Spades assembler assembly evaluation tool (quast)


Download spades assembler latest version 3.15.5 from official website


Download spades assembler previous versions from GitHub repository


Download spades assembler example data sets and reference genomes


Subscribe to spades assembler updates and news via email or Twitter


Provide feedback and bug reports to spades assembler developers via email or GitHub issues


Learn more about spades assembler features and algorithms from SPAdes papers and protocols


wget SPAdes-3.15.5-Darwin.tar.gz


Alternatively, you can use a web browser to download it manually. After downloading, you need to extract the file using the following command:


tar -xzf SPAdes-3.15.5-Darwin.tar.gz


This will create a folder named SPAdes-3.15.5-Darwin, which contains the executable files and other resources for SPAdes.


Downloading SPAdes source code




If you prefer to compile SPAdes from source code, or if you are using a different operating system, you can download the source code from the website as well. The file name is SPAdes-3.15.5.tar.gz. You can use the following command to download it:


wget


Alternatively, you can use a web browser to download it manually. After downloading, you need to extract the file using the following command:


tar -xzf SPAdes-3.15.5.tar.gz


This will create a folder named SPAdes-3.15.5, which contains the source code and other resources for SPAdes.


To compile SPAdes from source code, you need to have some prerequisites installed on your system, such as CMake, GCC, Python 2 or 3, zlib, bzip2, and Boost libraries. You can check the detailed instructions on how to install these prerequisites on the SPAdes website: . Once you have installed the prerequisites, you can use the following commands to compile SPAdes:


cd SPAdes-3.15.5 ./spades_compile.sh


This will create an executable file named spades.py in the bin folder.


Installing SPAdes




After downloading and extracting (or compiling) SPAdes, you need to install it on your system. The installation process is very simple and straightforward. You just need to add the bin folder of SPAdes to your system's PATH variable, so that you can run SPAdes from any directory.


Installing SPAdes on Linux




If you are using a Linux system, you can add the bin folder of SPAdes to your PATH variable by editing your .bashrc file (or equivalent) in your home directory. You can use the following command to open the file with a text editor (such as nano):


nano /.bashrc


Then, add the following line at the end of the file (replace /path/to/SPAdes-3.15.5-Linux/bin with the actual path of your SPAdes bin folder):


export PATH=$PATH:/path/to/SPAdes-3.15.5-Linux/bin


Save and close the file, and then run the following command to apply the changes:


source /.bashrc


You can now run SPAdes from any directory by typing spades.py.


Installing SPAdes on Mac




If you are using a Mac system, you can add the bin folder of SPAdes to your PATH variable by editing your .bash_profile file (or equivalent) in your home directory. You can use the following command to open the file with a text editor (such as nano):


nano /.bash_profile


Then, add the following line at the end of the file (replace /path/to/SPAdes-3.15.5-Darwin/bin with the actual path of your SPAdes bin folder):


export PATH=$PATH:/path/to/SPAdes-3.15.5-Darwin/bin


Save and close the file, and then run the following command to apply the changes:


source /.bash_profile


You can now run SPAdes from any directory by typing spades.py.


Verifying SPAdes installation and running a self-test




After installing SPAdes, you should verify that it works properly on your system. You can do this by running a self-test that comes with SPAdes. The self-test will run SPAdes on a small dataset and check if the output matches the expected results.


To run the self-test, you need to go to the test folder of SPAdes, which is located inside the main SPAdes folder. You can use the following command to go there:


cd /path/to/SPAdes-3.15.5/test


Then, you can run the self-test by typing:


./spades.py --test


This


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