Christian Brandt

Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques

This paper provides an overview and analysis of nanopore sequencing, offering guidelines to address challenges and maximize information gain from the technology.

Targeted decontamination of sequencing data with CLEAN

The paper introduces CLEAN, a pipeline to remove contaminants from sequencing data, improving reproducibility and analysis quality.

Accurate and Reproducible Whole-Genome Genotyping for Bacterial Genomic Surveillance with Nanopore Sequencing Data

This paper evaluates recent improvements in Oxford Nanopore sequencing for bacterial genomic surveillance, showing that new software tools significantly enhance accuracy and reproducibility.

Decoding bacterial methylomes in four public health-relevant microbial species: Nanopore sequencing enables reproducible analysis of DNA modifications

This study uses Nanopore sequencing to analyze DNA methylation in four bacterial species, identifying species-specific and novel methylation motifs and improving basecalling accuracy for reliable methylation detection.

Diversification of Pseudomonas aeruginosa biofilm populations under repeated phage exposures decreases the efficacy of the treatment

This study shows that repeated phage exposure to P. aeruginosa biofilms reduces phage efficacy due to genetic changes that confer resistance and tolerance.

Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors

This study evaluates Oxford Nanopore sequencing for outbreak tracing, identifies methylation-induced errors, and proposes a masking workflow to improve accuracy.

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing

This study evaluates Oxford Nanopore's adaptive sequencing for improving microbial sequencing yield in human vaginal samples by selectively depleting host DNA.

What the Phage: A scalable workflow for the identification and analysis of phage sequences

What the Phage provides a scalable, parallel workflow for phage sequence identification and analysis using multiple prediction tools and downstream annotation.

DarkQ: Continuous genomic monitoring using message queues

DarkQ enables instant sharing and discovery of newly sequenced genomes through a message queue system to improve timely access for stakeholders.

poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing

Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)

MUFFIN is a metagenomics workflow that integrates short and long reads to produce high-quality bins and annotations for microbial community analysis.

Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content

The paper introduces a method to reduce large genome collections by grouping similar genomes using embeddings, improving metagenomic classification accuracy.