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agc

Assembled Genomes Compressor

agc-istream

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

alignment-writer

Compact Themisto pseudoalignment files using BitMagic.

assembly-stats

Get assembly statistics from FASTA and FASTQ files

baby-microbiome-paper-plots

bacpop-website

Code for group website

bib-s-aureus-example

Example of using BIB to identify Staphylococcus aureus strains

biobins

Scripts for building distributable binaries of various bioinformatics software.

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfo-scripts

A collection of miscellaneous bioinformatics scripts.

bitseq

BitSeq code

blastfrost

bxzstr

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

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

cxxargs

Header-only command-line parsing library for C++11.

cxxio

Error-checking wrapper for working with files and directories in c++.

demix_check

fastspar

Rapid and scalable correlation estimation for compositional data

fulgor

A fast and compact k-mer index for large-scale matching and color queries.

ggcat

Compacted and colored de Bruijn graph construction and querying

gunc

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

introduction-to-applied-bioinformatics

Bacterial strain identification from sequencing data

kallisto

Near-optimal RNA-Seq quantification

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