Plasmid detection and assembly in genomic and metagenomic data sets

Antipov, Dmitry; Raiko, Mikhail; Lapidus, Alla; Pevzner, Pavel A.

doi:10.1101/gr.241299.118

Cited by 135 publications

(136 citation statements)

References 34 publications

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“…Thus, the key advantage of mosaicFlye over existing assembly tools lies in reconstructing the accurate sequences of repeat copies and a relatively small reduction in the number of contigs. However, these improvements are important, for example, long bacterial repeats often correspond to important sequences such as 16s rRNAs (Yuan et al, Bioinformatics 2015) or antibiotic resistance genes (Antipov et al, 2019). To benchmark mosaicFlye, we applied it to multiple datasets with complex repeats that the state-of-the-art long-read genome assemblers failed to resolve.…”

Section: Resultsmentioning

confidence: 99%

mosaicFlye: Resolving long mosaic repeats using long error-prone reads

Pevzner

2020

Preprint

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Long-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes. However, the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of bacterial genomes and metagenomes. We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of the human genome as well as bacterial genomes and metagenomes. In particular, we show that mosaicFlye results in a complete assembly of both arms of the human chromosome 6.

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Section: Resultsmentioning

confidence: 99%

mosaicFlye: Resolving long mosaic repeats using long error-prone reads

Pevzner

2020

Preprint

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“…Many bioinformatic tools have been recently developed to overcome this challenge in short-read sequencing. Examples of them are PlasmidFinder, cBar, PLACNET, (meta)plasmidSPAdes, recycler, plasflow, MOB-suite, mlplasmids, plaScope, gplas, plasClass, plasGUN,SCAPP, metaviralSPAdes ( Zhou and Xu, 2010 ; Carattoli et al., 2014 ; Rozov et al., 2017 ; Vielva et al., 2017 ; Arredondo-Alonso et al., 2018 ; Arredondo-Alonso et al., 2020 ; Krawczyk et al., 2018 ; Robertson and Nash, 2018 ; Royer et al., 2018 ; Antipov et al., 2019 , 2020 ; Fang et al., 2020 ; Pellow et al., 2020a , Pellow et al., 2020b ; Pellow et al., 2020 , 2020 ). These tools identify plasmids and viruses in metagenomic samples or bacterial isolates in a variety of ways, ranging from the simpler approach of blasting against a plasmid database (PlasmidFinder, MOB-suite) to the use of more complex deep neural networks (cBar, PlasFlow).…”

Section: Methods For Mobile Genetic Elements Analysis In Environmentamentioning

confidence: 99%

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

2020

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Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

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“…There are a number of tools that can be used to assemble or detect plasmids in isolate bacterial samples, such as plasmidSPAdes (Antipov et al, 2016), PlasmidFinder (Carattoli et al, 2014), cBar (Zhou and Xu, 2010), gPlas (Arredondo-Alonso et al, 2019), and others. However, there are currently only two tools that attempt to reconstruct complete plasmid sequences in metagenomic samples: Recycler (Rozov et al, 2017) and metaplasmidSPAdes (Antipov et al, 2019). Here we present SCAPP (Sequence Contents Aware Plasmid Peeler), a new algorithm building on Recycler that leverages external biological knowledge about plasmid sequences.…”

Section: Introductionmentioning

confidence: 99%

SCAPP: An algorithm for improved plasmid assembly in metagenomes

Pellow

Zorea

Probst

et al. 2020

Preprint

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Motivation: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids, which are less studied or understood. In order to assist in the study of these plasmids we developed SCAPP (Sequence Contents Aware Plasmid Peeler) -an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. Results: SCAPP builds on some key ideas from the Recycler plasmid assembly algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome that we generated. We also created a parallel plasmidome-metagenome cow rumen sample and used it to create a novel assessment procedure. In most cases SCAPP performed better than or similar to Recycler and meta-plasmidSPAdes across this wide range of datasets. Availability: https://github.com/Shamir-Lab/SCAPP

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Plasmid detection and assembly in genomic and metagenomic data sets

Cited by 135 publications

References 34 publications

mosaicFlye: Resolving long mosaic repeats using long error-prone reads

mosaicFlye: Resolving long mosaic repeats using long error-prone reads

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

SCAPP: An algorithm for improved plasmid assembly in metagenomes

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