ArticlemSystems2022
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.bioRxiv : the preprint server for biology · 2026Article
- Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.BMC genomics · 2026Article
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.Microbiology spectrum · 2025Article
- Environmental and Maternal Imprints on Infant Gut Metabolic Programming.bioRxiv : the preprint server for biology · 2025Article
- Article
- A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.mSystems · 2025Article
- Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.Microorganisms · 2025Article
- Clinical translation of microbiome research.Nature medicine · 2025Review
- Article
- Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.Nature communications · 2025Article
- The microbiome diversifiesbioRxiv : the preprint server for biology · 2024Article
- Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.Research square · 2024Article
- Article
- A simple solid media assay for detection of synergy between bacteriophages and antibiotics.Microbiology spectrum · 2024Article
- Transforming Big Data into AI-ready data for nutrition and obesity research.Obesity (Silver Spring, Md.) · 2024Review
- Oral Supplementation with the Short-Chain Fatty Acid Acetate Ameliorates Age-Related Arterial Dysfunction in Mice.Aging biology · 2024Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
Increasing data volumes on high-throughput sequencing instruments such as the NovaSeq 6000 leads to long computational bottlenecks for common metagenomics data preprocessing tasks such as adaptor and primer trimming and host removal. Here, we test whether faster recently developed computational tools (Fastp and Minimap2) can replace widely used choices (Atropos and Bowtie2), obtaining dramatic accelerations with additional sensitivity and minimal loss of specificity for these tasks. Furthermore, the taxonomic tables resulting from downstream processing provide biologically comparable results. However, we demonstrate that for taxonomic assignment, Bowtie2's specificity is still required. We suggest that periodic reevaluation of pipeline components, together with improvements to standardized APIs to chain them together, will greatly enhance the efficiency of common bioinformatics tasks while also facilitating incorporation of further optimized steps running on GPUs, FPGAs, or other architectures. We also note that a detailed exploration of available algorithms and pipeline components is an important step that should be taken before optimization of less efficient algorithms on advanced or nonstandard hardware.
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