Source files created during the Master's Thesis
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Updated
Feb 6, 2023 - Python
Source files created during the Master's Thesis
Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification
An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.
Minimiser-based digital normalisation for long-read DNA sequence datasets
a molecular solutions toolbox for molecular biologists.
Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
Accurate, resource-frugal and deterministic DNA sequence classifier.
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
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