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Plasmid identification software tools | Shotgun metagenomic sequencing data analysis

Plasmids have important roles in antibiotic resistance and in affecting production of metabolites used in industrial and agricultural applications. However, their extraction through deep sequencing remains challenging, in spite of rapid drops in cost and throughput increases for sequencing.

Source text:
(Rozov et al., 2016) Recycler: an algorithm for detecting plasmids from de novo assembly graphs. Bioinformatics.

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PlasFlow
Determines bacterial plasmid sequences in genomic and metagenomic assemblies. PlasFlow is an open source software, based on a deep neural network model that distinguishes plasmids and chromosomes. It can be applied to any assembly, including those without raw sequencing data. The program can be used for: (i) predicting phyla and supplying information related to taxons contributing to the plasmidome in a given environment (ii) identifying plasmid sequences carrying genes involved in heavy-metal resistance, (iii) analyzing large plasmids and megaplasmids.
plasmidSPAdes
A software tool for assembling plasmids from whole genome sequencing data. plasmidSPAdes utilizes SPAdes for transforming the de Bruijn graph into the assembly graph and finds a subgraph of the assembly graph that we refer to as the plasmid graph. It further uses ExSPAnder for repeat resolution in the plasmid graph using paired reads and generates plasmidic contigs. plasmidSPAdes does not require any specialized sample preparation to isolate plasmids, it has a potential to increase the throughput of plasmid discovery. It thus complements the recently published approach that is mainly aimed at analyzing plasmids after plasmid isolation.
PlasmidFinder
Allows identification of plasmids in total or partial sequenced isolates of bacteria. PlasmidFinder is based on a curated database of plasmid replicons intended for the identification of plasmids in whole-genome sequences originating from Enterobacteriaceae species. The web application provides the detection of replicons in the whole genome sequencing (WGS) but also assigns the plasmids under study to lineages that trace back the information to the existing knowledge on Inc groups and suggests possible reference plasmids for each lineage.
Plasmid Profiler
Provides comparative plasmid content analysis. Plasmid Profiler is a comparative pipeline for visualization of plasmid content in whole genome sequencing (WGS) data from bacterial isolates. It identifies plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. Users can query plasmids for genes or regions of interest and visualize results as an interactive heat map.
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