karel-brinda

Karel Břinda's starred repositories

carbon-lang

Carbon Language's main repository: documents, design, implementation, and related tools. (NOTE: Carbon Language is experimental; see README)

Language:C++NOASSERTION32258 391 593

The-Art-of-Linear-Algebra

Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

Language:PostScriptCC0-1.016583 141 14

Data-Science-Cheatsheet

Language:TeX2517 130 8

mccortex

De novo genome assembly and multisample variant calling

Language:CMIT112 15 91

cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

Language:RustMIT110 6 1

cobs

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

Language:C++MIT82 11 19

sshash

A compressed, associative, exact, and weighted dictionary for k-mers.

Language:C++MIT81 5 21

metaMDBG

MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.

Language:C++MIT80 4 10

spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences

Language:C++GPL-2.072 2 63

kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections

Language:C++AGPL-3.068 5 30

rust-debruijn

De Bruijn graphs in Rust

Language:RustMIT62 24 4

ssubmit

Submit slurm sbatch jobs without a script

Language:RustUnlicense61 2 3

langmead-lab

Publicly-visible Langmead Lab resources

60 50

gwfa

Proof-of-concept implementation of GWFA for sequence-to-graph alignment

Language:CMIT55 40

Verticall

Recombination-free trees

Language:PythonGPL-3.054 4 4

sketchy

Genomic neighbor typing of bacterial pathogens using MinHash :rat:

Language:RustMIT43 7 54

lv89

C implementation of the Landau-Vishkin algorithm

Language:C++MIT35 3 4

kff-reference

Contains the description of a file format to store kmers and associated values

AGPL-3.030 5 4

sfasta

Language:RustMIT27 5 2

kff-tools

Language:C++AGPL-3.017 4 9

PAC

Language:C++GPL-3.010 4 4

cpp-app-template

Language:CMakeAGPL-3.07 10

rase-pipeline

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

Language:PythonMIT6 3 9

mbgc

Multiple Bacteria Genome Compressor (MBGC)

Language:CGPL-3.0600

rase

The core RASE package

Language:PythonMIT500

satcomp

Language:PythonApache-2.05 40

kmer-ology

Language:Jupyter Notebook5 30

gsearch

Approximate nearest neighbour search for microbial genomes based on hash metric

Language:RustMIT200

tree_order_evaluation

Evaluating Hierarchical Clustering Methods for Corpora with Chronological Order

Language:PythonGPL-3.0200

HumanGenome

How compressible is a human genome sequence?

Language:ShellGPL-3.0000