PUB - Publikationen an der Universität Bielefeld

**Motivation:** Plasmids are ubiquituous in bacterial genomes, and have been shown to be involved in important evolutionary processes, in particular the acquisition of antimicrobial resistance. However separating chromosomal contigs from plasmid contigs and assembling the later is a challenging problem. **Results:** We introduce HyAsP, a tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm. We test HyAsP on a large sample of bacterial data sets and observe that it generally outperforms other tools. **Availability:** https://github.com/cchauve/HyAsP. **Supplementary information:** Supplementary text and data are available at Bioinformatics online.