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Hector Isaev
Hector Isaev

SPAdes: A Toolkit for Genome Assembly with Various Data Types


Spades Genome Assembler Download: A Guide for Beginners




Genome assembly is the process of reconstructing the complete DNA sequence of an organism from short fragments of sequencing data. It is a challenging computational problem that requires sophisticated algorithms and software tools. Genome assembly is essential for studying the structure, function, evolution, and diversity of genomes, as well as for applications in biotechnology, medicine, and agriculture.




spades genome assembler download


Download: https://www.google.com/url?q=https%3A%2F%2Ft.co%2FCAMgxJypGZ&sa=D&sntz=1&usg=AOvVaw0Ykjltgd-icfxxDu_sNJJB



Spades genome assembler is one of the most popular and widely used tools for genome assembly. It is a de novo assembler that can handle various types of sequencing data, such as Illumina, IonTorrent, PacBio, Oxford Nanopore, and Sanger. Spades can also perform hybrid assembly using multiple data sources, as well as specialized assembly for metagenomes, plasmids, transcripts, biosynthetic gene clusters, and viruses. Spades has been shown to produce high-quality assemblies with high contiguity and completeness.


How to download spades genome assembler




Spades genome assembler is freely available under the GPLv2 license and can be downloaded from . There are different ways to download spades depending on your operating system and preferences.


Downloading spades binaries for Linux or Mac




The easiest way to download spades is to use the pre-compiled binaries for Linux or Mac. You can find the latest version of spades (3.15.5) in the following links:


  • for Linux (64-bit only)



  • for Mac



To install spades from the binaries, you need to download the corresponding file, extract it, and add the bin directory to your PATH environment variable. For example, on Linux you can do:


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wget


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


export PATH=$PATH:$PWD/SPAdes-3.15.5-Linux/bin


Downloading and compiling spades source code




If you prefer to compile spades from the source code, you need to download the source code file from and follow the instructions in the README.md file. You will need a C++ compiler (gcc >= 5.3.1 or clang >= 3.8), cmake (>= 2.8), zlib, bzip2, and Python (>= 2.7) libraries installed on your system.


To compile spades from the source code, you need to download the file, extract it, create a build directory, run cmake, and run make. For example, on Linux you can do:


wget


tar -xzf SPAdes-3.15.5.tar.gz


cd SPAdes-3.15.5


mkdir build


cd build


make


make install


Verifying the installation




To verify that spades is installed correctly, you can run the following command:


spades.py --test


This will run a test assembly on a small dataset and check the results. If everything is OK, you should see a message like this:


======= SPAdes pipeline finished.


SPAdes log can be found here: /home/user/SPAdes-3.15.5/build/spades_test/corrected/configs/config.info


Thank you for using SPAdes!


How to use spades genome assembler




Spades genome assembler is a command-line tool that takes sequencing data as input and produces assembly files as output. To use spades, you need to know the type and format of your input data, the options and parameters that control the assembly process, and the output files and formats that spades generates.


Input data types and formats




Spades can handle various types of sequencing data, such as:


  • Illumina paired-end (PE) or mate-pair (MP) reads



  • IonTorrent PE or MP reads



  • PacBio single-molecule real-time (SMRT) reads



  • Oxford Nanopore long reads



  • Sanger reads



  • Hybrid data from multiple sources



The input data should be in FASTA or FASTQ format, compressed or uncompressed. Spades can automatically detect the format of the input files, but you need to specify the type of the data using the following prefixes:


Data typePrefix


Illumina PE reads-1 and -2


Illumina MP reads-m1 and -m2


IonTorrent PE reads-i1 and -i2


IonTorrent MP reads-mi1 and -mi2


PacBio SMRT reads--pacbio


Oxford Nanopore long reads--nanopore


Sanger reads--sanger


Hybrid data from multiple sourcesUse multiple prefixes accordingly


Command line options and parameters




Spades has many command line options and parameters that can be used to customize the assembly process. Some of the most important ones are:


  • -o: the output directory where spades will store the assembly files



  • -k: the k-mer sizes to use for assembly (comma-separated list of odd numbers between 21 and 127)



  • --careful: the mode to reduce the number of mismatches and short indels in the assembly



  • --only-assembler: the mode to skip error correction and read filtering steps



  • --cov-cutoff: the coverage cutoff value to discard low-covered and high-covered k-mers



  • --meta: the mode to perform metagenomic assembly



  • --plasmid: the mode to perform plasmid assembly



  • --rna: the mode to perform transcriptome assembly



  • --gene-finding: the option to enable gene prediction on the assembled contigs



  • --help: the option to display the help message with all the available options and parameters



For example, to run spades on Illumina PE reads with k-mer sizes of 21, 33, and 55, in careful mode, with a coverage cutoff of 10, and gene finding enabled, you can use the following command:


spades.py -1 reads_1.fq -2 reads_2.fq -k 21,33,55 --careful --cov-cutoff 10 --gene-finding -o output_dir


Output files and formats




Spades produces several output files and formats in the output directory specified by the -o option. Some of the most important ones are:


  • spades.log: the log file that contains information about the spades run, such as parameters, steps, timings, and errors



  • corrected/: the directory that contains the error-corrected reads (if error correction is enabled)



  • assembly_graph.fastg: the file that contains the assembly graph in FASTG format



  • scaffolds.fasta: the file that contains the final scaffolds in FASTA format



  • contigs.fasta: the file that contains the final contigs in FASTA format



  • genes/: the directory that contains the predicted genes on the contigs (if gene finding is enabled)



You can use these files for further analysis and evaluation of your assembly.


How to evaluate the quality of the assembly




Evaluating the quality of the assembly is an important step to assess how well spades performed on your data. There are different tools and metrics that can be used to evaluate the quality of the assembly, such as:


  • Quast: a tool that computes various assembly statistics, such as number of contigs, N50, GC content, and misassemblies. You can download quast from and run it on your assembly file using the following command:



quast.py scaffolds.fasta -o quast_output


  • Comparative genome viewer: a tool that visualizes the alignment of the assembly to a reference genome or another assembly. You can use tools such as Mauve, IGV, or Bandage to compare and explore your assembly graphically. For example, you can download Mauve from and run it on your assembly file and a reference genome file using the following command:



mauve scaffolds.fasta reference.fasta


GenomeQC: a tool that compares the assemblies and annotations of different genomes and reports the quality score


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