SPAdes specifications

Information


Unique identifier OMICS_01502
Name SPAdes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Paired-end reads, mate-pairs and single (unpaired) reads
Input format FASTA, FASTQ, unmapped BAM
Output data Reads corrected by BayesHammer, resulting contigs and scaffolds, SPAdes assembly graph, paths in the assembly graph corresponding to contigs and scaffolds results
Output format FASTA, FASTG
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.10.1
Stability Stable
Requirements Illumina, IonTorrent or PacBio, g++, cmake zlib, libbz
Source code URL http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz
Maintained Yes

Subtools


  • SPADES genome assembler
  • BAYESHAMMER
  • ExSPAnder
  • dipSPAdes
  • truSPAdes
  • rnaSPAdes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Sergey I. Nikolenko <>
  • person_outline Andrey D. Prjibelski <>

Additional information


http://bioinf.spbau.ru/spades/

SPAdes articles

SPAdes citations

 (9)
2018
PMCID: 5773742

[…] run. the genome library was prepared according to nextera kit instructions, and the library quality was analyzed in a bioanalyzer 2010 (agilent technologies). genome assembly was performed using the spades genome assembler (6), and the quality was analyzed using quast 4.1 (7). for genome annotation, the ncbi prokaryotic genome annotation pipeline was used (8). in the draft genome of b. subtilis […]

2017
PMCID: 5647799

[…] and z. ardabiliae, were also analyzed. there are five z. pseudotritici strains and four z. ardabiliae strains first described in stukenbrock etal. (2011). de novo assembly was performed using spades with four different k-mers (21, 33, 55, and 77) (bankevich etal. 2012). the assembled genomes are available upon request. the statistics of genome assembly is shown in supplementary table s2, […]

2017
PMCID: 5597766

[…] seq platform using a miseq version 3 reagent kit (illumina). the reads were quality trimmed using the sliding window mode of the trimmomatic program (8). de novo genome assembly was performed using a spades genome assembler (st. petersburg genome assembler version 3.9.0) (9). the draft sequence consists of 181 contigs of more than 200 bp, with an average coverage of 22.0×, an n50 length of 45,496  […]

2017
PMCID: 5618209

[…] with plants and target pathogens and pests, we sequenced the whole genome of the strain item 908. the genome was sequenced on an ion s5 platform generating around 7 m bpand assembled using the spades v5.0 software. the resulting genome sequence has an estimated size of 39,131,654 bp. the reference gene sequences of its and tef1 were extracted from the genome assembly. the identification […]

2017
PMCID: 5492696

[…] in the sequence read archive (sra) at the national center for biotechnology information (ncbi) under the bioproject prjna368735. draft de novo genome assembly of paired-end reads was performed using spades v.2.4.0 (bankevich et al., 2012) with pre-assembly bayeshammer read correction, default k-mer size testing options, and post-assembly burrows wheeler aligner mismatch correction. contigs […]

SPAdes institution(s)
Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia; Theodosius Dobzhansky Center for Genome Bioinformatics; St. Petersburg State University, St. Petersburg, Russia; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA; DOE Joint Genome Institute, Walnut Creek, CA, USA; J. Craig Venter Institute, La Jolla, CA, USA; Department of Mathematics, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
SPAdes funding source(s)
This work was supported by the Government of the Russian Federation grant 11.G34.31.0018, the U.S. National Institutes of Health (NIH) grant 3P41RR024851-02S1, 1R01GM095373 and 2R01HG003647, the U.S. National Science Foundation (NSF) grant CCF-1115206, OCE-1148017, OCE-821374, and OCE-1019242, the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231, the Alfred P. Sloan Foundation grant 2007-10-19

SPAdes reviews

 (3)
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Korin Albert

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I have been using SPAdes 3.9.1. for all my de novo genome assemblies. It's easy to use so I suggest trying it if you are new to bioinformatics. This is the first command-line program I learned. Use Bandage after it runs to view a graph of the assembly quality and get some summary info.

senaj

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Easy to use.