ArticleGenes2021
Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.
Article in Genes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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
72 citing papers in PubMed.
- Genomic structure ofMicrobial genomics · 2026Article
- HighMicrobiology spectrum · 2026Article
- Up-to-date MALDI-TOF MS-based identification of theJournal of clinical microbiology · 2026Article
- Antimicrobial resistance in breeding pigs in Germany - differences between 2015 and 2023.Porcine health management · 2026Article
- Large outbreak ofEpidemiology and infection · 2026Article
- Genomic epidemiology ofJournal of clinical microbiology · 2026Observational
- Antimicrobial resistance of commensal and extended-spectrum ß-lactamase/AmpC-producing Escherichia coli in organic meat chicken farms.Poultry science · 2026Article
- Article
- Phylodynamic analysis ofMicrobial genomics · 2026Article
- Complete genome of a cereulide-producingMicrobiology resource announcements · 2026Article
- Impact of sequencing read quality on whole-genome sequencing outcomes for foodborne pathogens using a BacWORK standardized analysis workflow.Bioinformatics advances · 2026Article
- Nanopore sequencing in suitcase lab enables improved detection ofFrontiers in microbiology · 2026Article
- Article
- A new member of the novel, non-core Brucella clade: An exotic frog isolate closely related to atypical Brucella isolates from recent human brucellosis cases in Australia.BMC microbiology · 2025Article
- Increased occurrence ofOne health (Amsterdam, Netherlands) · 2025Article
- The Gene Ail for the Attachment-Invasion Locus Protein ofInternational journal of molecular sciences · 2025Article
- Development and validation of a core genome multilocus sequence typing scheme forJournal of clinical microbiology · 2025Article
- Evaluation of expert rules for carbapenemase class identification inJournal of clinical microbiology · 2025Article
- A multi-isolate genomic approach identifies diverseMicrobial genomics · 2025Article
- Fibre supplementation alters the gastrointestinal microbiome, the microbial metabolites and indicators of neurodegeneration in a mouse model of Alzheimer´s disease.Scientific reports · 2025Article
12 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance of many microorganisms. An increasing number of laboratories are currently in a transition phase from classical methods towards next generation sequencing, generating unprecedented amounts of data. Since the precision of downstream analyses depends significantly on the quality of raw data generated on the sequencing instrument, a comprehensive, meaningful primary quality control is indispensable. Here, we present AQUAMIS, a Snakemake workflow for an extensive quality control and assembly of raw Illumina sequencing data, allowing laboratories to automatize the initial analysis of their microbial whole-genome sequencing data. AQUAMIS performs all steps of primary sequence analysis, consisting of read trimming, read quality control (QC), taxonomic classification, de-novo assembly, reference identification, assembly QC and contamination detection, both on the read and assembly level. The results are visualized in an interactive HTML report including species-specific QC thresholds, allowing non-bioinformaticians to assess the quality of sequencing experiments at a glance. All results are also available as a standard-compliant JSON file, facilitating easy downstream analyses and data exchange. We have applied AQUAMIS to analyze ~13,000 microbial isolates as well as ~1000 in-silico contaminated datasets, proving the workflow's ability to perform in high throughput routine sequencing environments and reliably predict contaminations. We found that intergenus and intragenus contaminations can be detected most accurately using a combination of different QC metrics available within AQUAMIS.
Indexed as
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.