ArticleMicrobiome2019
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers, 1 of them a synthesis that pooled it.
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Who cites it
150 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Impact of Dietary Interventions on the Microbiota in Inflammatory Bowel Disease: A Systematic Review.Journal of Crohn's & colitis · 2024Pooled it
- Antimicrobial-resistant organism carriage and metagenomic characterization of the microbiome and resistome in veterinary workers.Veterinary research communications · 2026Article
- Early-life colonization withScience (New York, N.Y.) · 2026Article
- Senescence-associated loss of intestinal α1,2-fucose disrupts a modifiable host-microbiome homeostasis axis in people with HIV.bioRxiv : the preprint server for biology · 2026Article
- Microbial and immune determinants of disease severity and death in pediatric pneumonia.medRxiv : the preprint server for health sciences · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Gut microbiome in preterm infants with different weight gain outcomes.Gut microbiology · 2026Article
- Probiotic supplementation for anxiety symptoms in people with Parkinson's disease: a randomized, double-blind, placebo-controlled trial.NPJ Parkinson's disease · 2026Article
- The naked mole-rat microbiome is associated with healthy aging and social structure.Cell reports · 2026Article
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- Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.Microbiome · 2026Article
- IntratumoralScience advances · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection.Nature communications · 2026Article
- HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.GigaScience · 2026Article
- Review
- Compositional maturation of the microbiome and adaptive immunity in the postnatal period.Frontiers in immunology · 2026Article
- Integrated epidemiologic investigation and genomic confirmation of a Klebsiella pneumoniae neonatal sepsis outbreak in Botswana.PLOS global public health · 2026Article
90 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundAnalysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes.
resultsWe present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated.
conclusionsSunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.