Skip to main content

RFPlasmid Predicting plasmid contigs

Project description

RFPlasmid Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers

Linda van der Graaf-van Bloois, Jaap Wagenaar, Aldert Zomer

Introduction: Antimicrobial resistant (AMR) genes in bacteria are often carried on plasmids. Since these plasmids can spread the AMR genes between bacteria, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. Whole genome sequence (WGS) analysis makes it easy to determine if a strain contains a resistance gene, however, it is not easy to determine if the gene is located on the chromosome or on a plasmid as genome sequence assembly generally results in 50-300 DNA fragments (contigs). With our newly developed prediction tool, we analyze the composition of these contigs to predict their likely source, plasmid or chromosomal. This information can be used to determine if a resistant gene is chromosomally located or on a plasmid. The tool is optimized for 19 different bacterial species, including Campylobacter, E. coli, and Salmonella, and can also be used for metagenomic assemblies.

Methods: The tool identifies the number of chromosomal marker genes, plasmid replication genes and plasmid typing genes using CheckM and DIAMOND Blast, and determines pentamer frequencies and contig sizes per contig. A prediction model was trained using Random Forest on an extensive set of plasmids and chromosomes from 19 different bacterial species and validated on separate test sets of known chromosomal and plasmid contigs of the different bacteria. Results: Prediction of plasmid contigs was nearly perfect when calculated based on number of correctly predicted bases, with up to 99% specificity and 99% sensitivity. Prediction of small contigs remains difficult, since these contigs consists primarily of repeated sequences present in both plasmid and chromosome, e.g. transposases.

Conclusion: The newly developed tool is able to determine if contigs are chromosomal or plasmid with a very high specificity and sensitivity (up to 99%) and can be very useful to analyze WGS data of bacterial genomes and their antimicrobial resistance genes.

A web-interface to test single fasta files is available here: http://klif.uu.nl/rfplasmid/

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release.See tutorial on generating distribution archives.

Built Distribution

rfplasmid-0.0.11-py3-none-any.whl (52.0 MB view details)

Uploaded Python 3

File details

Details for the file rfplasmid-0.0.11-py3-none-any.whl.

File metadata

  • Download URL: rfplasmid-0.0.11-py3-none-any.whl
  • Upload date:
  • Size: 52.0 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.15.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/45.2.0 requests-toolbelt/0.9.1 tqdm/4.40.2 CPython/3.5.2

File hashes

Hashes for rfplasmid-0.0.11-py3-none-any.whl
Algorithm Hash digest
SHA256 f0a451f1586f210880652e6645986a49ad23fd510443a2a45296bc2a5e604819
MD5 5bc9e1703ea71e716cab40d6499a1c81
BLAKE2b-256 35b9ed718d1dc05f1d84dd4cb999f9ffad07ffb7121b5b3f2cc3677c7325d05b

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page