karel-brinda

Phylign

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

NanoSim-H

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

MiniPhy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

attotree

tp-zpevnik

Zpěvník Technické přestávky. Výsledné (automaticky generované) zpěvníky se nachází na http://karel-brinda.github.io/tp-zpevnik/.

de-MiniPhy-BIGSIdata

Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs

bin

Miscellaneous scripts, configuration files, and sample documents

galitime

simplitigs-supplementary

Data and pipelines for Simplitigs as an efficient and scalable representation of de Bruijn graphs

unprotect-docx

Bash script to unprotect password-protected unencrypted DOCX documents.

citation-styles

cpp-app-template

docx2pdf

f-masked-superstrings-supplement

fmsi

FMSI is an exact f-masked-sueprstrings-based index for membership queries and set operations on k-mer sets.

ganttrify

Create beautiful Gantt charts with ggplot2

human-genome-compression

jarvis2

Efficient DNA sequence compression

karel-brinda

kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

masked-superstrings-supplement

Packages

phylogenetic-compression-supplement

Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

plascad

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

rase

The core RASE package

rase-db-ngonorrhoeae-gisp

rase-db-skeleton

rase-pipeline

RASE pipeline for inferring antibiotic resistance and susceptibility using genomic neighbor typing.

satcomp

xz

:floppy_disk: Free general-purpose data compression software with high compression ratio.