Plasmid identification software tools | Shotgun metagenomic sequencing data analysis

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.

Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.

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.

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.

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.

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.

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.