ArticlemSystems2020
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 223 papers.
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Who cites it
223 citing papers in PubMed.
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- Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.Applied and environmental microbiology · 2026Article
- Viral genetic diversity and functional potential in polar and subarctic sea ice.FEMS microbiology ecology · 2026Article
- Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.FEMS microbiology ecology · 2026Article
- Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.Microbial ecology · 2026Article
- Distance-Limited Larval Replenishment in the Deep-Sea Mussel Gigantidas platifrons Challenges Connectivity-Based Conservation Planning.Molecular ecology · 2026Article
- Different Ferromanganese Concretion Morphologies Host Distinct Microbial Communities and Metal Accumulation Patterns in the Baltic Sea.Environmental microbiology · 2026Article
- Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.mSystems · 2026Article
- Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.BMC genomics · 2026Article
- Assessing the diversity and functional profile of the "microbial proteome" in fermented foods.Food & function · 2026Article
- Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).BMC genomics · 2026Article
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- The evolution of gene functional repertoire in Amorphea: divergent strategies across Amoebozoa, Fungi, and Metazoa.Molecular biology and evolution · 2026Article
- Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily.Nature communications · 2026Article
- Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.Communications biology · 2026Article
163 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual.
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