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.
Programs search nucleotide databases by using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison. Users can select an optimization according to: (i) highly similar sequences, (ii) more dissimilar sequences or (iii) somewhat similar sequences. This web application proceeds by searching sets in NCBI data sources.
Identifies, visualizes and analyzes plasmids in whole genome sequencing (WGS) projects by creating a network of contig interactions. PLACNET uses three types of information to identify plasmids: (i) information about scaffold links and coverage in the WGS assembly, (ii) comparison to reference plasmid sequences, and (iii) plasmid-diagnostic sequence features such as replication initiator proteins.
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.
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.
A tool designed for extracting circular sequences from de novo assembly graphs. Recycler can be applied on isolate as well as metagenome and plasmidome data. The circular sequences it outputs may be plasmids, phages, etc. Recycler uses only features of the assembly graph (contig overlaps, lengths, and coverage level information) and alignments of paired-end reads to the contigs in the graph in order to identify these sequences.
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.
Enables the detection of plasmids from bacterial whole genome sequencing (WGS) data without read assembly. PlasmidSeeker is a tool that allows detection of known plasmid sequences from unassembled raw WGS reads. Moreover, this tool is able to estimate copy numbers of these known plasmids and is suitable to utilize as a first step in the analysis of plasmid content.
Provides a method for plasmid and chromosome classification of E. coli contigs. PlaScope is based on the metagenomic classifier Centrifuge that exploits exact matches and small-sized databases. This software has the specificity to select a unique assignment of contigs to plasmid, chromosome or unclassified. It uses location of contigs to classify and fits to identify operons like aerobactin and salmochellin that can be on plasmid and chromosome.
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.
Assists in heterologous candidate enzymes selection. Selenzyme is an online tool which query a target reaction. It can accept multiple queries from any other web-based application. It provides enzyme selection solutions in different scenarios such as the selection of enzyme sequences.
Identifies sequence representing mobile genetic elements (MGEs). PlasmidTron is a tool that utilizes the phenotypic data such as antibiograms, virulence factors, or geographic information. It can be used to assemble reads from each sample linked by a phenotype. This tool allows users to reconstruct all of the sequences of plasmid responsible for a particular phenotype.
Detects plasmid-derived and chromosome-predicted contigs for three bacterial species: Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli. mlplasmids is based on a set of machine-learning classifiers fitted to the investigated species. The application can be run as a web application which includes additional functions for filtering the results by minimum sequence length or minimum posterior probability.
Assists users in distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. cBAR was developed to classify a given metagenome into chromosomal and plasmid sequences, based on observed differences in their pentamer frequencies. This method is based on a sequential minimal optimization (SMO) model which separates chromosomal from plasmid sequences.