Accurate, resource-frugal and deterministic DNA sequence classifier.
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Updated
Jun 1, 2024 - Python
Accurate, resource-frugal and deterministic DNA sequence classifier.
Thesis projects
A Rust library providing fully dynamic sets of k-mers with high locality
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.
Phage-Host Interaction Search Tool
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
A compressor for k-mers sets with counters
Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs
Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
ProPhex – an exact k-mer index using Burrows-Wheeler Transform
Project for the course of Bioinformatics - University of Padua.
counts k-mers, written in rust
Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"
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