SPAdes protocols

View SPAdes computational protocol

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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
  • IonHammer
  • rnaSPAdes
  • SPADES genome assembler
  • truSPAdes

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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

 (538)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] surveillance and eradication campaigns conducted in slaughter plants., the 164 mtbc strains used to compare the m. bovis strains from uruguay were downloaded from public databases, assembled with spades [], and annotated with prokka []. the pan genome of all the 186 strains was estimated with roary (v3.6.8) []; core genes were defined as those present in all 186 isolates with a 90% id […]

2018
PMCID: 5754475
PMID: 29301895
DOI: 10.1128/genomeA.00839-17

[…] lp (shallowater, tx) using an illumina miseq (2 × 300 bp) platform. the raw reads were checked for quality and adapter contamination using trim galore () and then assembled into contigs using a spades genome assembler (). dna ends were conformed via pcr. genes were predicted using genemark () and were manually annotated using the ncbi protein nr database. the family of phage tyrion […]

2018
PMCID: 5754480
PMID: 29301900
DOI: 10.1128/genomeA.01292-17

[…] of 4 bp and minimum phred score of 30 was applied. subsequent read quality was assessed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and assembly was performed using spades genome assembler v3.9.0 (). an average genome coverage of 1,254× for phage apc_jm3.2 was achieved. putative phage coding sequences were identified using prodigal v1.20 (), and functions […]

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

[…] the raw sequences were preprocessed using cutadapt version 1.14 to trim adaptors () and using prinseq version 0.20.4 to perform quality filtering (). initial genome assembly was performed with the spades version 3.10.0 genome assembler program (). 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: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] linkage clustering followed by visualization of the resulting dendrograms and manual removal of any outliers. reads mapping to contigs within each genome bin were extracted and reassembled using spades () with the “-careful” flag enabled. a final scaffolding step was performed using sspace (). final draft genome completeness and contamination was assessed using checkm (). the final draft […]


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SPAdes in publications

 (1274)
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] high sensitivity dna kit. paired-end 250 nt reads were generated using miseq v2 chemistry on an illumina miseq at the university of technology sydney. de novo genome assembly was carried out using spades v3.9 using the—careful flag to reduce potential misassembly events. maxbin v2.2.1 was used to cluster contigs according to abundance and gc content, thereby separating chlamydial […]

PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18

[…] by using a nextera xt kit and sequenced by using a version 3 600-cycle kit on a miseq sequencer (illumina), yielding 4,047,156 quality-filtered paired-end reads., de novo assembly of the reads using spades () recovered a large alloherpesvirus-related contig, which was joined to other contigs manually by pcr and sanger sequencing. the reads were assembled against the resulting contig by using […]

PMCID: 5946047
PMID: 29748400
DOI: 10.1128/genomeA.00329-18

[…] of each strain (va-wgs-00333: weslaco; va-wgs-00353: singapore) were verified using the in silico salmonella serotype prediction tool seqsero version 1.0 (). de novo assemblies were generated using spades version 3.9.0 (), and annotation of the draft genomes was performed using the ncbi prokaryotic genome annotation pipeline (pgap) ()., quality of the de novo assemblies was assessed using quast […]

PMCID: 5946039
PMID: 29748407
DOI: 10.1128/genomeA.00396-18

[…] miseq v3 reagent kit. this sequencing resulted in 1,006,529 paired-end reads. low-quality reads/bases were filtered using trimmomatic version 0.36 (), and de novo assembly was performed using spades version 3.10.1 (). the resulting genome comprised 21 contigs of 3,332,539 bp. the average genome coverage of the paired-end reads was 121×. the maximum contig length was 701,368 bp. the draft […]

PMCID: 5946038
PMID: 29748411
DOI: 10.1128/genomeA.00411-18

[…] paired end) by gatc biotech ag (constance, germany). raw sequences were trimmed for quality using sickle 1.33 (parameters, q > 30; 1 > 45) (). the cleaned sequences were then assembled using spades 3.10.0 (). contigs obtained from the assembly were therefore curated for length (>500 bp) and coverage (>10×) to ensure no errors and contamination in the draft genome. the contigs […]


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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.