Article CC BY 4.0
refereed
published

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.

ORCID
0000-0002-2509-4950
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Deneke, Carlus;
ORCID
0000-0002-7710-3011
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Brendebach, Holger;
ORCID
0000-0002-6020-3841
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Uelze, Laura;
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Borowiak, Maria;
ORCID
0000-0002-3363-8225
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Malorny, Burkhard;
ORCID
0000-0002-6874-233X
Affiliation
German Federal Institute for Risk Assessment (BfR), Department 4 Biological Safety, Study Centre 4SZ - Genome Sequencing and Analysis, Germany
Tausch, Simon H

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.

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