ArticleMicrobiome2014
PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Article in Microbiome, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
155 citing papers in PubMed, 1 synthesis or guideline pooled it, 270 citations in OpenAlex.
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- Effects of Supplementing Yeast Culture to Prepartum Cows Under Heat Stress on the Jejunal Microbiota and Metabolites of Calves.Animals : an open access journal from MDPI · 2026Article
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- Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.Evolutionary applications · 2026Article
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
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- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Gut microbiota-regulated unconjugated bilirubin metabolism drives renal calcium oxalate crystal deposition.Gut microbes · 2025Article
- Microbial Dynamics in a Musalais Wine Fermentation: A Metagenomic Study.Foods (Basel, Switzerland) · 2025Article
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- Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.Blood advances · 2025Observational
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
95 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 at 3 institutions in 1 country.
Funding
Abstract
backgroundRecent innovations in sequencing technologies have provided researchers with the ability to rapidly characterize the microbial content of an environmental or clinical sample with unprecedented resolution. These approaches are producing a wealth of information that is providing novel insights into the microbial ecology of the environment and human health. However, these sequencing-based approaches produce large and complex datasets that require efficient and sensitive computational analysis workflows. Many recent tools for analyzing metagenomic-sequencing data have emerged, however, these approaches often suffer from issues of specificity, efficiency, and typically do not include a complete metagenomic analysis framework.
resultsWe present PathoScope 2.0, a complete bioinformatics framework for rapidly and accurately quantifying the proportions of reads from individual microbial strains present in metagenomic sequencing data from environmental or clinical samples. The pipeline performs all necessary computational analysis steps; including reference genome library extraction and indexing, read quality control and alignment, strain identification, and summarization and annotation of results. We rigorously evaluated PathoScope 2.0 using simulated data and data from the 2011 outbreak of Shiga-toxigenic Escherichia coli O104:H4.
conclusionsThe results show that PathoScope 2.0 is a complete, highly sensitive, and efficient approach for metagenomic analysis that outperforms alternative approaches in scope, speed, and accuracy. The PathoScope 2.0 pipeline software is freely available for download at: http://sourceforge.net/projects/pathoscope/.
Identifiers
What OpenQuestion holds
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.