SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

Aytan-Aktug, Derya; Grigorjev, Vladislav; Szarvas, Judit; Clausen, Philip C.; Munk, Patrick; Nguyen, Marcus; Davis, James J.; Aarestrup, Frank M.; Lund, Ole

doi:10.1128/spectrum.02641-22

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

Journal Article · Tue Nov 15 00:00:00 EST 2022 · Microbiology Spectrum

DOI:https://doi.org/10.1128/spectrum.02641-22· OSTI ID:1984973

^[1]; Grigorjev, Vladislav ^[1]; ^[1]; ^[1]; ^[1]; ^[2]; ^[2]; ^[1]; ^[1]

Technical Univ. of Denmark, Lyngby (Denmark)
Univ. of Chicago, IL (United States); Argonne National Laboratory (ANL), Argonne, IL (United States). Data Science and Learning Division; Northwestern Univ., Evanston, IL (United States). Northwestern-Argonne Institute for Science and Engineering (NAISE)

High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/).

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institutes of Health (NIH); Novo Nordisk Foundation; USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1984973

Journal Information:: Microbiology Spectrum, Journal Name: Microbiology Spectrum Journal Issue: 6 Vol. 10; ISSN 2165-0497

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring blaNDM-1: a comparative genomic analysis of carbapenem resistant strains Pajand, Omid; Rahimi, Hamzeh; Badmasti, Farzad figshare https://doi.org/10.6084/m9.figshare.24037228	image	January 2023
Additional file 2 of Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring blaNDM-1: a comparative genomic analysis of carbapenem resistant strains Pajand, Omid; Rahimi, Hamzeh; Badmasti, Farzad figshare https://doi.org/10.6084/m9.figshare.24037231.v1	dataset	January 2023
Additional file 3 of Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring blaNDM-1: a comparative genomic analysis of carbapenem resistant strains Pajand, Omid; Rahimi, Hamzeh; Badmasti, Farzad figshare https://doi.org/10.6084/m9.figshare.24037234	dataset	January 2023

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59 BASIC BIOLOGICAL SCIENCES
assembly identification
bacteriophage
chromosome
machine learning
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source identification

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

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