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
Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"
Projet GENOM master 2 BIM : 2022 - 2023 Projet de bio-informatique sur les k-mers codé en Python
Mutation table of COVID-19 virus genome with all possible substitution mutations and corresponding 20-mers for mutation identification
Project for the course of Bioinformatics - University of Padua.
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.
A compressor for k-mers sets with counters
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
Get Started with DNA Sequencing working with .FastQ and .FastA file formats and performing Pattern Matching Algorithms (Exact & Approximate).
Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs
Investigating genome size variation with k-mers
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
ProPhex – an exact k-mer index using Burrows-Wheeler Transform
simple virus DNA classification
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.
Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
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