Indexing & querying large assembly graphs -- in space, no one can hear you miao!
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Updated
Feb 1, 2024 - Standard ML
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
A method for variant graph genotyping based on exact alignment of k-mers
ProphAsm – a rapid computation of simplitigs directly from k-mer sets
Accurate, resource-frugal and deterministic DNA sequence classifier.
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
counts k-mers, written in rust
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
Phage-Host Interaction Search Tool
Get Started with DNA Sequencing working with .FastQ and .FastA file formats and performing Pattern Matching Algorithms (Exact & Approximate).
An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.
ProPhex – an exact k-mer index using Burrows-Wheeler Transform
Thesis projects
Source files created during the Master's Thesis
simple virus DNA classification
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