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Updated: Jul 12, 2026
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
nf-core/magmap: Map metatranscriptomes to large collections of genomes.
Danilo Di Leo1, Emelie Nilsson1, George Westmeijer2
1Centre for Ecology and Evolution in Microbial Model Systems-, EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden.
Bioinformatics (Oxford, England)
|July 10, 2026
Summary
The nf-core/magmap pipeline facilitates genome-resolved metatranscriptome analysis by enabling mapping to public or private reference genomes. This reproducible workflow enhances the study of prokaryotic and eukaryotic communities.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Metatranscriptome annotation traditionally relies on direct alignment or de novo assembly due to limited reference genomes.
- Increasing metagenomic data from natural environments enables genome-resolved approaches.
Purpose of the Study:
- To introduce the nf-core/magmap pipeline for reproducible metatranscriptome analysis.
- To provide a workflow for selecting, mapping to, and quantifying features from reference genomes.
Main Methods:
- The nf-core/magmap pipeline is implemented in Nextflow and is part of the nf-core collaboration.
- It supports reference genomes from public repositories or private collections.
- The pipeline is designed for prokaryotic communities but can be adapted for eukaryotes.
Main Results:
- The pipeline offers a reproducible, accessible, and well-documented workflow.
- Enables genome-resolved studies of metatranscriptomes.
- Facilitates quantification of features from selected reference genomes.
Conclusions:
- The nf-core/magmap pipeline addresses the need for efficient genome-resolved metatranscriptome analysis.
- It supports both prokaryotic and eukaryotic community studies.
- The pipeline enhances the utility of publicly available and private genome data.
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