PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

(2017) Alex Orlek et al.   Frontiers in Microbiology

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

(2017) Märt Roosaare et al.   PeerJ

plasmidSPAdes: assembling plasmids from whole genome sequencing data

(2016) Dmitry Antipov et al.   BIOINFORMATICS

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

(2016) Lena K. Nyberg et al.   Scientific Reports

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists

(2015) Lauris Kaplinski et al.   GigaScience

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One