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SPAdes | A genome assembly algorithm and its applications to single-cell sequencing

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide Additional contigs can also be provided to be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads and can take as input several paired-end and mate-pair libraries simultaneously.

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2 user reviews

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senaj

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Easy to use.

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bo zhang

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Very Good Support on Illumina Sequencing Data (PE150), especially with reference genome while assembly a novel strain.

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SPAdes classification

SPAdes specifications

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

Subtools

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

SPAdes distribution

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SPAdes support

Documentation

Maintainers

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

Additional information

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

Credits

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Publications

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

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

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