tmaklin

bxzstr

A C++ header-only ZLib / libBZ2 / libLZMA / Zstandard wrapper.

tigz

Parallel gzip decompression and compression using libdeflate and rapidgzip.

seamat

Templatized and parallelized matrix library for c++.

agc

Assembled Genomes Compressor

agc-istream

(wip) Read samples from agc archives using C++ iostreams.

biobins

Scripts for building distributable binaries of various bioinformatics software.

bioconda-recipes

Conda recipes for the bioconda channel.

assembly-stats

Get assembly statistics from FASTA and FASTQ files

bioinfo-scripts

A collection of miscellaneous bioinformatics scripts.

BlastFrost

clbtype

Screen assemblies for colibactin production and resistance genes.

coreutils_demix_check

Partial reimplementation of demix_check by @harry-thorpe without the python or R dependencies.

cpprate

Reimplementation of the variable selection via RATE method https://github.com/lorinanthony/RATE

ggcat

Compacted and colored de Bruijn graph construction and querying

gunc

Python package for detection of chimerism and contamination in prokaryotic genomes.

KMC

A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT

maklin.fi

Sources for my personal webpage https://maklin.fi Created using hugo.

Mash

Fast genome and metagenome distance estimation using MinHash

panaani

Pangenome-aware dereplication of bacterial genomes into ANI clusters.

parallel-processor-rs

Framework to manage asynchronous execution of multiple compute units communicating using messages

RabbitMash

RabbitMash: an efficient highly optimized implementation of Mash.

rcgpar

c++ library for parallel and distributed estimation of mixture model components using variational inference.

redsvd-h

Header-only version of RedSVD

server

The Etebase server (so you can run your own)

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

ska.rust

Split k-mer analysis – version 2

telescope

Library & executable for converting Themisto pseudoalignments to kallisto pseudoalignments.

tilastoseura.fi

Suomen Tilastoseuran verkkosivut

unmulti

Split a multifasta file into many fasta files containing a single sequence, or extract a list of sequences/contigs. Supports compressed input and output files.

vaaligp

Gaussian process poll aggregator for 2023 Finnish parlamentary election polling using Stan.