Details
| Original language | English |
|---|---|
| Article number | 748 |
| Number of pages | 12 |
| Journal | BMC Genomics |
| Volume | 23 |
| Issue number | 1 |
| Early online date | 11 Nov 2022 |
| Publication status | Published - Dec 2022 |
Abstract
Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende.
Keywords
- Absolute quantification, Genomics, Long-read metagenomics, Metagenomic visualization, Metagenomics
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biotechnology
- Biochemistry, Genetics and Molecular Biology(all)
- Genetics
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In: BMC Genomics, Vol. 23, No. 1, 748, 12.2022.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Wochenende
T2 - modular and flexible alignment-based shotgun metagenome analysis
AU - Rosenboom, Ilona
AU - Scheithauer, Tobias
AU - Friedrich, Fabian C.
AU - Pörtner, Sophia
AU - Hollstein, Lisa
AU - Pust, Marie Madlen
AU - Sifakis, Konstantinos
AU - Wehrbein, Tom
AU - Rosenhahn, Bodo
AU - Wiehlmann, Lutz
AU - Chhatwal, Patrick
AU - Tümmler, Burkhard
AU - Davenport, Colin F.
N1 - Funding Information: We would like to thank all tool authors for their professional contributions. Marie Dorda provided excellent technical assistance in the laboratory. We gratefully acknowledge the computing resources provided by the HPC-seq cluster at Hannover Medical School (initial funding by DFG Großgeräteantrag INST 192/514-1 FUGG). Funding Information: Open Access funding enabled and organized by Projekt DEAL. This work was supported by grants from the Deutsche Forschungsgemeinschaft (SFB900, projects A2 and Z1, project no. 158989968), from the Volkswagen-Stiftung and the Niedersächsisches Ministerium für Wissenschaft und Kultur (Big Data in the Life Sciences, project no. ZN3432) and the Bundesministerium für Bildung und Forschung (BMBF) for the Disease Area CF at the German Center for Lung Research (DZL) at BREATH, Hannover (project no. 82DZL002A1).
PY - 2022/12
Y1 - 2022/12
N2 - Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende.
AB - Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende.
KW - Absolute quantification
KW - Genomics
KW - Long-read metagenomics
KW - Metagenomic visualization
KW - Metagenomics
UR - http://www.scopus.com/inward/record.url?scp=85141663569&partnerID=8YFLogxK
U2 - 10.1101/2022.03.18.484377
DO - 10.1101/2022.03.18.484377
M3 - Article
C2 - 36368923
AN - SCOPUS:85141663569
VL - 23
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 748
ER -