1.
Bartoszewicz, J.M., Nasri, F., Nowicka, M., Renard, B.Y.: Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection. Bioinformatics. 38, ii168-ii174 (2022).
Emerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remain comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone.We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats.The neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1400 genomes with host and pathogenicity metadata supports training of machine-learning models and sequence comparison, not limited to the pathogen detection task.The data, models and code are hosted at https://zenodo.org/record/5846345, https://zenodo.org/record/5711877 and https://gitlab.com/dacs-hpi/deepac.Supplementary data are available at Bioinformatics online.
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AbstractEmerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remain comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone.We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats.The neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1400 genomes with host and pathogenicity metadata supports training of machine-learning models and sequence comparison, not limited to the pathogen detection task.The data, models and code are hosted at https://zenodo.org/record/5846345, https://zenodo.org/record/5711877 and https://gitlab.com/dacs-hpi/deepac.Supplementary data are available at Bioinformatics online.
2.
Ulrich, J.-U., Epping, L., Pilz, T., Walther, B., Stingl, K., Semmler, T., Renard, B.Y.: In-silico enrichment of bacterial plasmids by chromosomal depletion using nanopore adaptive sampling. bioRxiv. (2022).
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the small proportion of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We further inspect potential cost savings for laboratories by utilizing adaptive sampling on reused or expired flow cells. We show that a significant enrichment can be achieved even on reused or expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. Our experiments indicate that the choice of the read classification method and read lengths used for the classification influence the enrichment factor.Competing Interest StatementJUU and BYR have filed a patent application on selective nanopore sequencing approaches.
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AbstractBacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the small proportion of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We further inspect potential cost savings for laboratories by utilizing adaptive sampling on reused or expired flow cells. We show that a significant enrichment can be achieved even on reused or expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. Our experiments indicate that the choice of the read classification method and read lengths used for the classification influence the enrichment factor.Competing Interest StatementJUU and BYR have filed a patent application on selective nanopore sequencing approaches.
3.
Ulrich, J.-U., Lutfi, A., Rutzen, K., Renard, B.Y.: ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing. Bioinformatics. 38, i153-i160 (2022).
Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background.The C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer.Supplementary data are available at Bioinformatics online.
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AbstractNanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which cannot handle human-sized reference sequences, or apply read mapping in sequence space relying on fast graphical processing units (GPU) base callers for real-time read rejection. Using nanopore long-read mapping tools is also not optimal when mapping shorter reads as usually analyzed in adaptive sampling applications.Here, we present a new approach for nanopore adaptive sampling that combines fast CPU and GPU base calling with read classification based on Interleaved Bloom Filters. ReadBouncer improves the potential enrichment of low abundance sequences by its high read classification sensitivity and specificity, outperforming existing tools in the field. It robustly removes even reads belonging to large reference sequences while running on commodity hardware without GPUs, making adaptive sampling accessible for in-field researchers. Readbouncer also provides a user-friendly interface and installer files for end-users without a bioinformatics background.The C++ source code is available at https://gitlab.com/dacs-hpi/readbouncer.Supplementary data are available at Bioinformatics online.
