We are grateful to the mothers that participated in the study, the clinical teams at the Manhiça District Hospital, the Magude Health Center, and the Ilha Josina Health center, and the personnel at CISM and ISGlobal . We are also grateful to Dr. Deepak Gaur who offered very generously recombinant proteins produced in his lab.
Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UKUniversité de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, Inserm, 75015, Paris, FranceDepartment of Parasites & Insect Vectors, Malaria Parasite Biology and Vaccines, Institut Pasteur, Paris, FranceMalaria Group, International Centre for Genetic Engineering and Biotechnology , New Delhi, IndiaEusébio MaceteDepartment of Physiologic Sciences, Faculty of...
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Wochenende — modular and flexible alignment-based shotgun metagenome analysis - BMC GenomicsBackground 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 .
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