SPAdes statistics

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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
  • IonHammer
  • rnaSPAdes
  • SPADES genome assembler
  • truSPAdes

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Versioning


No version available

Documentation


Maintainers


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

Additional information


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

Publications for SPAdes

SPAdes citations

 (1312)
library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] th 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 and non-chlamy […]

call_split

Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany

2018
Genome Announc
PMCID: 5946050
PMID: 29748399
DOI: 10.1128/genomeA.00266-18
call_split See protocol

[…] quencing libraries were conducted using the Illumina Nextera XT DNA sample preparation kit. Raw read data were used for de novo genome assembling using the PATRIC database (https://patricbrc.org) (). SPAdes assembly calculations resulted in 10- to 20-fold sequence coverages per consensus sequence for all isolates. Genome annotation using the automated Prokaryotic Genome Annotation Pipeline (PGAP) […]

library_books

Draft Genome Sequence of Staphylococcus aureus Strain HD1410, Isolated from a Persistent Nasal Carrier

2018
Genome Announc
PMCID: 5946038
PMID: 29748411
DOI: 10.1128/genomeA.00411-18

[…] × 150 bp 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 were then an […]

library_books

Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia

2018
Genome Announc
PMCID: 5946047
PMID: 29748400
DOI: 10.1128/genomeA.00329-18

[…] s 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 ve […]

call_split

Genome Sequence of a Novel Alloherpesvirus Isolated from Glass Catfish (Kryptopterus bicirrhis)

2018
Genome Announc
PMCID: 5946053
PMID: 29748409
DOI: 10.1128/genomeA.00403-18
call_split See protocol

[…] ed 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 Bowt […]

library_books

High Quality Draft Single Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

2018
Genome Announc
PMCID: 5946040
PMID: 29748404
DOI: 10.1128/genomeA.00383-18

[…] ence Core Laboratory at the King Abdullah University of Science and Technology (KAUST). Thirty-two million reads were quality trimmed using Trimmomatic version 0.32 () and assembled into contigs with SPAdes version 3.9.0 (), applying the error correction and the single-cell mode. Genome completeness was estimated using CheckM ().The SAG is composed of 132 contigs totaling 1.42 Mbp (N50, 74.2 kbp; […]

Citations

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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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Desktop
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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Desktop
Easy to use.