AI Article Synopsis
- The study focuses on improving taxonomic binning in metagenome characterization through an optimized workflow involving reads mapping and taxonomic assignment.
- A statistical framework was developed to optimize mapper parameters and selection thresholds, which led to increased performance compared to default settings across various sequencing technologies.
- The findings were validated using a dataset from the Human Microbiome Project, demonstrating the effectiveness of the optimized configurations.
Article Abstract
Motivation: Alignment-based taxonomic binning for metagenome characterization proceeds in two steps: reads mapping against a reference database (RDB) and taxonomic assignment according to the best hits. Beyond the sequencing technology and the completeness of the RDB, selecting the optimal configuration of the workflow, in particular the mapper parameters and the best hit selection threshold, to get the highest binning performance remains quite empirical.
Results: We developed a statistical framework to perform such optimization at a minimal computational cost. Using an optimization experimental design and simulated datasets for three sequencing technologies, we built accurate prediction models for five performance indicators and then derived the parameter configuration providing the optimal performance. Whatever the mapper and the dataset, we observed that the optimal configuration yielded better performance than the default configuration and that the best hit selection threshold had a large impact on performance. Finally, on a reference dataset from the Human Microbiome Project, we confirmed that the optimized configuration increased the performance compared with the default configuration.
Availability And Implementation: Not applicable.
Contact: magali.dancette@biomerieux.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btw040 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.
Microbiome
December 2024
Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Department of Bioinformatics and Systems Biology, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
Background: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.
Results: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms.
Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.
PLoS One
December 2024
Research and Internationalisation Office, National University of Science and Technology, Bulawayo, Zimbabwe.
The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe.
View Article and Find Full Text PDFThe Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod () as Determined by Shotgun DNA Sequencing.
Microorganisms
October 2024
Department of Chemistry and the Center for Bioinformatics, Faculty of Science and Technology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
Article Synopsis
- Animals, along with their microbial communities, are called metaorganisms, but many species' microbial diversity is still understudied.
- This study used shotgun DNA sequencing to analyze the microbial composition of the gut mucus in Northeast Arctic cod and compared it with their fecal microbiota.
- Results showed three distinct taxonomic profiles in the gut mucus, indicating a unique and diverse microbial population separate from the more uniform bacteria found in their feces.
rIDIMS: A novel tool for processing direct-infusion mass spectrometry data.
Talanta
March 2025
BIOINOVAR - Biotechnology Laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-902, Brazil. Electronic address:
Article Synopsis
- Metabolomics using mass spectrometry (MS) is gaining traction due to its efficiency and minimal sample prep, but a lack of user-friendly applications hinders those without programming skills.
- To address this issue, rIDIMS is introduced as a browser-based tool that streamlines the workflow for processing MS data, allowing users to easily conduct analyses and generate customizable reports.
- The tool has been tested in various cases, including coffee bean classification and lipid profiling for health studies, showcasing its potential to enhance reproducibility and reliability in metabolomic research.
Detection of diagnostic somatic copy number alterations from cerebrospinal fluid cell-free DNA in brain tumor patients.
Acta Neuropathol Commun
November 2024
Dr. Senckenberg Institute of Neurooncology, University Hospital, Goethe University Frankfurt, Frankfurt, Germany.
Article Synopsis
- The study investigates the use of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) as a less invasive alternative to brain biopsies for diagnosing brain tumors and addressing tumor heterogeneity.
- A total of 33 CSF samples were collected from 30 patients, and shallow whole-genome sequencing was performed, revealing significant somatic copy number aberrations (SCNAs) in brain tumor patients' cfDNA.
- The findings suggest that cfDNA analysis can effectively identify relevant genomic alterations, offering insights into tumor evolution and heterogeneity, thus enhancing diagnostic accuracy for CNS cancers.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!