Wochenende — modular and flexible alignment-based shotgun metagenome analysis

• DOI: 10.1186/s12864-022-08985-9
• Publication Date: 2022-11-11T05:16:32Z
• Authors: Ilona Rosenboom; Tobias Scheithauer; Fabian C. Friedrich; Sophia Pörtner; Lisa Hollstein; Marie-Madlen Pust; Konstantinos Sifakis; Tom Wehrbein; Bodo Rosenhahn; Lutz Wiehlmann; Patrick Chhatwal; Burkhard Tümmler; Colin F. Davenport
• Keywords: Normalization; Shotgun; Database normalization

Abstract Background Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome of fungal, viral, archaeal bacterial taxonomy, particularly with regard to visualization read mapping location, normalization options, growth dynamics functional gene repertoires. Current classification tools use non-standard output formats, or do not fully show information on location. As reference datasets are perfect, portrayal is critical judging results effectively. Results Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters normalization. completely transparent can be adjusted by the user. We observe stringent filtering mismatches sharply reduces number false positives. Further modules allow genomic calculation rates, as well integration subsequent plotting pipeline heatmaps heat trees. novel approach additionally allows absolute abundance profiles comparison reads assigned human host genome. Conclusion Wochenende has ability find filter alignments all kingdoms life using both short long reads, requires only good genomes. automatically combines multiple available ranging from control taxonomic visualization. at https://github.com/MHH-RCUG/nf_wochenende .