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metaSPAdes: a new versatile metagenomic assembler.

作者信息

Nurk Sergey, Meleshko Dmitry, Korobeynikov Anton, Pevzner Pavel A

机构信息

Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia 199004.

Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia 198515.

出版信息

Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15.


DOI:10.1101/gr.213959.116
PMID:28298430
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5411777/
Abstract

While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/3ee070805724/824f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/cc552b8fcd3d/824f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/4928de21c859/824f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/9d8ba75ca3cd/824f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/76e582f32cb3/824f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/3ee070805724/824f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/cc552b8fcd3d/824f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/4928de21c859/824f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/9d8ba75ca3cd/824f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/76e582f32cb3/824f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/71d8/5411777/3ee070805724/824f05.jpg

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本文引用的文献

[1]
Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome.

Sci Rep. 2016-9-29

[2]
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.

Methods. 2016-6-1

[3]
Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community.

Front Microbiol. 2016-2-2

[4]
Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

mBio. 2016-2-9

[5]
TruSPAdes: barcode assembly of TruSeq synthetic long reads.

Nat Methods. 2016-2-1

[6]
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.

Nat Biotechnol. 2016-1

[7]
MetaQUAST: evaluation of metagenome assemblies.

Bioinformatics. 2015-11-26

[8]
hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Bioinformatics. 2016-4-1

[9]
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

Front Bioeng Biotechnol. 2015-9-17

[10]
Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria.

J Nat Prod. 2015-7-24

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