ArticleBMC bioinformatics2018
SAMSA2: a standalone metatranscriptome analysis pipeline.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.The Journal of nutritional biochemistry · 2020Trial
- Adaptive Response ofAntibiotics (Basel, Switzerland) · 2026Article
- Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body.Nature biotechnology · 2026Article
- Linking composition and function: a two-year metatranscriptomic study of microbial adaptation in an industrial wastewater treatment plant.FEMS microbiology ecology · 2026Article
- Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.Environmental microbiome · 2026Article
- Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation.Environmental microbiology reports · 2026Article
- Article
- RTTAP: Empowering metatranscriptomic data analysis with a read-based total-infectome taxonomic solution.iMetaOmics · 2025Article
- Emergent roles of infant gut microbes during the utilization of human milk oligosaccharides.NPJ biofilms and microbiomes · 2025Article
- Bismuth subsalicylate profoundly alters gut microbiome and immunity with increased susceptibility to infection.medRxiv : the preprint server for health sciences · 2025Article
- A capsular polysaccharide from a healthy human microbiota member activates a Lag-3-NK cell axis to restrain colon cancer and augment immunotherapy.Cell reports · 2025Article
- metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.BMC bioinformatics · 2025Article
- Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science.Metabolites · 2025Review
- Metatranscriptomics reveals gene expression dynamics during an anatoxin-a producing Dolichospermum bloom in a western coastal lake.Chemosphere · 2025Article
- Metatranscriptomes of activated sludge microbiomes from saline wastewater treatment plant.Scientific data · 2025Article
- The Dentin Microbiome: A Metatranscriptomic Evaluation of Caries-Associated Bacteria.Biomedicines · 2025Article
- Article
- Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.ISME communications · 2025Article
- Microbial survival strategies in desiccated roots ofFrontiers in microbiology · 2025Article
- The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.PeerJ · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundComplex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms.
resultsSAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.
conclusionsSAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.
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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.