SPAdes protocols

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


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

Download


Versioning


Add your version

Documentation


Maintainers


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

Additional information


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

Publications for SPAdes

SPAdes IN pipelines

 (19)
2018
PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17

[…] raw sequences were preprocessed using cutadapt version 1.14 to trim adaptors (10) and using prinseq version 0.20.4 to perform quality filtering (11). initial genome assembly was performed with the spades version 3.10.0 genome assembler program (12). contigs less than 1,000 bp in length and with a coverage depth lower than 10× were excluded, which resulted in 15 contigs with a combined total […]

2018
PMCID: 5786680
PMID: 29371354
DOI: 10.1128/genomeA.01517-17

[…] (illumina, san diego, ca, usa). quality filtering was performed using trimmomatic version 0.32 (6) and resulted in 2,866,928 paired-end reads. de novo genome assembly was performed with the spades genome assembler version 3.8.0 (7). the assembly resulted in 101 contigs (>500 bp), with an average coverage of 93×. the assembly was validated and the read coverage determined […]

2018
PMCID: 5794933
PMID: 29437086
DOI: 10.1128/genomeA.00011-18

[…] by the manufacturer (illumina, san diego, ca, usa). quality filtering using trimmomatic version 0.32 (7) resulted in 2,714,322 paired-end reads. de novo genome assembly was performed with the spades genome assembler version 3.8.0 (8). the assembly resulted in 96 contigs (>500 bp) and an average coverage of 87-fold. the assembly was validated and the read coverage determined […]

2018
PMCID: 5794942
PMID: 29437095
DOI: 10.1128/genomeA.01520-17

[…] reads. sequencing primers were removed using cutadapt (5) and low-quality read regions were trimmed using sickle (https://github.com/najoshi/sickle). illumina reads were de novo assembled using spades 3.7.1 (6). contigs shorter than 200 bp were discarded. the resulting nuclear genome assembly had a length of 11,611,250 bp divided into 561 contigs; the n50 contig length was 62,127 bp. […]

2017
PMCID: 5282449
PMID: 28197136
DOI: 10.3389/fmicb.2017.00073

[…] the most hits from a sample. to produce a de novo whole genome assembly from sequence reads matching the nov database bins were concatenated and concatenated reads were assembled into contigs using spades (bankevich et al., 2012)., additionally, the previously identified closed genome with the highest number of associated reads was then used in a reference guided assembly using smalt v 0.7.4 […]

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.