Fredrik Boulund

lldap. Light LDAP implementation

shelfmark. Python

grimmory. A self-hosted library for your ebooks, comics, and audiobooks

bookorbit. BookOrbit: Your Reading Space

Calibre-Web-Automated. Calibre-Web but Automated and with tons of New Features! Fully automate and simplify your eBook set up!

gickup. Go

nWave. AI agents that guide you from idea to working code, with you in control at every step.

AdGuardHome. Network-wide ads & trackers blocking DNS server

copyparty. Portable file server with accelerated resumable uploads, dedup, WebDAV, SFTP, FTP, TFTP, zeroconf, media indexer, thumbnails++ all in one file

duckdb. DuckDB is an analytical in-process SQL database management system

x360ce. Primary repository for the x360ce library, front-end and tools.

bichon. Bichon – A lightweight, high-performance Rust email archiver with WebUI

yggdrasil-go. An experiment in scalable routing as an encrypted IPv6 overlay network

nebula. A scalable overlay networking tool with a focus on performance, simplicity and security

best-of-typst. 🏆 A ranked list of awesome projects related to Typst, or the charted dark matter in Typst Universe (TCDM). 🌌

tessera_typ. A Typst package for combining multiple images into masonry or matrix layout.

FlyOOBE. Fly through your Windows 11 setup 🐝

Ventoy. A new bootable USB solution.

AMBER. Analyzing Mapping Biases and Evaluating Read Reliability

linear-algebra. A concise, beginner-friendly introduction to the core ideas of linear algebra.

embed-pdf-viewer. A PDF viewer that seamlessly integrates with any JavaScript project

radEmu. R

zed. Code at the speed of thought – Zed is a high-performance, multiplayer code editor from the creators of Atom and Tree-sitter.

Selins. Selector of Influential Subcompositions (Selins) algorithm, screen and filter data to identify significant subcompositions. Selins sets the selection threshold in a fully data-driven manner, adapting the CsCsHM statistic for optimal signal detection in sparse, two-component mixture models.

infrastructure-resources. Infrastructure resources

home-assistant-floor-plan. Home Assistant Floor Plan Generator Plugin For Sweet Home 3D

koreader. An ebook reader application supporting PDF, DjVu, EPUB, FB2 and many more formats, running on Cervantes, Kindle, Kobo, PocketBook and Android devices

jazz2-native. 🎮 · Jazz² Resurrection: Native C++ reimplementation of Jazz Jackrabbit 2

jazz2. 🎮 · Jazz² Resurrection: Open-source reimplementation of Jazz Jackrabbit 2

docs. Docs is an open-source text editor: web-native, made for real-time collaboration, cleanly structured documents and sub-documents with full ownership of your data. Built to scale with Django and React.

laptop. anyon_e, a highly integrated, high end, open source laptop. Attempt the impossible.

docker-libgourou. dockerized version of libgourou (free implementation of Adobe's ADEPT protocol used to manage DRM in ePub/PDF files). ACSM, Adobe Digital Editions, WINE-free

libgourou. libgourou is a free implementation of Adobe's ADEPT protocol used to add DRM on ePub/PDF files… forked from https://indefero.soutade.fr/p/libgourou

knock. Convert ACSM files to DRM-free EPUB files with one command on Linux

usearch12. Open-source usearch

DiscoGrad. DiscoGrad - automatically differentiate across conditional branches in C++ programs

Stirling-PDF. #1 PDF Application on GitHub that lets you edit PDFs on any device anywhere

awesome-genome-visualization. A list of interesting genome browser and genome visualization programs

xESP32-Faikout. ESP32 based module to control Daikin aircon units

BACTpipe. BACTpipe: An assembly and annotation pipeline for bacterial genomics

bactopia. A flexible pipeline for complete analysis of bacterial genomes

fleece. A super-fast, compact, JSON-equivalent binary data format

ivy. Convert Machine Learning Code Between Frameworks

igv-reports. Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

mgs2amr. R

carnelian. Python

NEMO. NEMO is a laboratory logistics web application. Use it to schedule reservations, control tool access, track maintenance issues, and more.

openfortivpn. Client for PPP+TLS VPN tunnel services

MAP2B. Shell

Metabuli. Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

fhex. A Full-Featured HexEditor compatible with Linux/Windows/MacOS

conterminator. Detection of incorrectly labeled sequences across kingdoms

StrainXpress. StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high complexity metagenome sequencing data at strain resolution.

CheckM2. Assessing the quality of metagenome-derived genome bins using machine learning

Semaphore. A full-body keyboard using gestures to type through computer vision

sniffnet. Comfortably monitor your Internet traffic 🕵️‍♂️

refine. A React Framework for building internal tools, admin panels, dashboards & B2B apps with unmatched flexibility.

stag-mwc. StaG Metagenomic Workflow Collaboration

audioFlux. A library for audio and music analysis, feature extraction.

mercury. Impress your boss and turn a Jupyter notebook into a beautiful, shareable web app — no callbacks, no frontend, no rewrite.

smk-simple-slurm. A simple Snakemake profile for Slurm without --cluster-config

amr. AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

AMRplusplus. AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.

GuitarEffects. A low latency guitar effects processor suitable for running on a raspberry pi

hugo-scroll. Clean, responsive, single-page Hugo website theme.

bakta. Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

PhiSpy. Prediction of prophages from bacterial genomes

paper-age. Easy and secure paper backups of secrets

minixfromscratch. Development and compilation setup for the book versions of MINIX (2.0.0 and 3.1.0) on QEMU

memories. Fast, modern and advanced photo management suite. Runs as a Nextcloud app.

sra-human-scrubber. An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

spyglass. A personal search engine: Create a searchable library from your personal documents, interests, and more!

strobealign. Aligns short reads using dynamic seed size with strobemers

carbonyl. Chromium running inside your terminal

portable-secret. Better privacy without special software

infisical. Infisical is the open-source platform for secrets, certificates, and privileged access management.

slurm. Cookiecutter for snakemake slurm profile

amrplusplus_v2. MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data

shillelagh. Making it easy to query APIs via SQL

slackdump. Save or export your private and public Slack messages, threads, files, and users locally without admin privileges.

pydamage. Damage parameter estimation for ancient DNA

krakenuniq. 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

MOSCA. Meta-Omics Software for Community Analysis

quantpi. Microbiome profiling

kraken2-server. Kraken2 Server

Graphite. Community-built comprehensive 2D content creation appplication for graphic design, digital art, and interactive real-time motion graphics powered by a node-based procedural graphics engine

penpot. Penpot: The open-source design platform for Product teams that need scalable collaboration.

copy-dialog-lunar-lander. Play lunar lander in you windows file copy dialog

daikin_residential. Cloud control of Daikin devices that are supported by Daikin Residential Controller app.

metapi. A general metagenomics data mining system focus on robust microbiome research

plumber. Turn your R code into a web API.

the_cyber_plumbers_handbook. Free copy of The Cyber Plumber's Handbook - The definitive guide to Secure Shell (SSH) tunneling, port redirection, and bending traffic like a boss.

inthe.am. Access your Taskwarrior tasks from any browser anywhere

pyhmmer. Cython bindings and Python interface to HMMER3.

spec. The canonical spec for ulid

kmcp. Accurate metagenomic profiling && Fast large-scale sequence/genome searching

brename. A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression

rush. A cross-platform command-line tool for executing jobs in parallel

kraken2_classification. Snakemake workflow for metagenomic classification with Kraken2

pure-bash-bible. 📖 A collection of pure bash alternatives to external processes.

jo. JSON output from a shell

litestar. Light, flexible and extensible ASGI framework | Built to scale

red-mail. Advanced email sending for Python

docarray. Represent, send, store and search multimodal data

fastapi-mvc. Developer productivity tool for making high-quality FastAPI production-ready APIs.

keeweb. Free cross-platform password manager compatible with KeePass

mealie. Mealie is a self hosted recipe manager and meal planner with a RestAPI backend and a reactive frontend application built in Vue for a pleasant user experience for the whole family. Easily add recipes into your database by providing the url and mealie will automatically import the relevant data or add a family recipe with the UI editor

recipes. Application for managing recipes, planning meals, building shopping lists and much much more!

mold. mold: A Modern Linker 🦠

mitre. The Microbiome Interpretable Temporal Rule Engine

DeDRM_tools. DeDRM tools for ebooks

scientific-visualization-book. An open access book on scientific visualization using python and matplotlib

github-ci. An example GitHub Action (CI) to build a Singularity container

useful-sed. Useful sed scripts & patterns.

score-assemblies. Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

magic-wormhole. get things from one computer to another, safely

PowerToys. Microsoft PowerToys is a collection of utilities that supercharge productivity and customization on Windows

lba2-classic. Assembly

lba1-classic. Assembly

MMHP_SOP_rmhost. Python

sqlmodel. SQL databases in Python, designed for simplicity, compatibility, and robustness.

TreeViewer. Cross-platform software to draw phylogenetic trees

tuplex. Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code. Tuplex has similar Python APIs to Apache Spark or Dask, but rather than invoking the Python interpreter, Tuplex generates optimized LLVM bytecode for the given pipeline and input data set.

hAMRonization. Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

docker-redmine. Docker Image for Redmine

superset-reverse-nginx-example. a small working example of using superset with a base url using nginx' reverse proxy

devops-exercises. Linux, Jenkins, AWS, SRE, Prometheus, Docker, Python, Ansible, Git, Kubernetes, Terraform, OpenStack, SQL, NoSQL, Azure, GCP, DNS, Elastic, Network, Virtualization. DevOps Interview Questions

vaultwarden. Unofficial Bitwarden compatible server written in Rust, formerly known as bitwarden_rs

flameshot. Powerful yet simple to use screenshot software :desktop_computer: :camera_flash:

restic-pg-dump-docker. Docker image that backs up PostgreSQL to S3 via restic.

vim-mundo. :christmas_tree: Vim undo tree visualizer

WatchosGrande. Watchos Grande, the cheesy simple process watchdog

pgmodeler. Open-source data modeling tool designed for PostgreSQL. No more typing DDL commands. Let pgModeler do the work for you!

restic-windows-backup. Powershell scripts to run Restic backups on Windows

seaweedfs. SeaweedFS is a distributed storage system for object storage (S3), file systems, and Iceberg tables, designed to handle billions of files with O(1) disk access and effortless horizontal scaling.

photoprism. AI-Powered Photos App 🌈💎✨

restic. Fast, secure, efficient backup program

duplicacy. A new generation cloud backup tool

runcer-necromancer. script for data recovery for interrupted runs on MGISEQ-2000 (now DNBSEQ-G400)

pupperware. Container fun time lives here.

fastapi. FastAPI framework, high performance, easy to learn, fast to code, ready for production

miniLIMS. LIMS in development to be used in NGS facility

commonlims. Common LIMS is a generic plugin based LIMS system (in alpha)

parse_kraken2_report. Taxonomically informed parsing of kraken2 report output.

horcrux. Split your file into encrypted fragments so that you don't need to remember a passcode

clarity-ext. Extensions for Clarity

SneakerNet. :feet: QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run

SARS-CoV-2_Sequencing. A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

concatfs. concatfs FUSE driver for easy file concatenation (like large movie files)

videos. Lecture video processing scripts 🎥

RaGOO. RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

plotnine. A Grammar of Graphics for Python

hmmer. HMMER: biological sequence analysis using profile HMMs

Metalign. Metalign: efficient alignment-based metagenomic profiling via containment min hash

DamageProfiler. A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage

qurro. Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

DEICODE. Robust Aitchison PCA from sparse count data

localstack. 💻 A fully functional local AWS cloud stack. Develop and test your cloud & Serverless apps offline

metaeuk. MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

senaite.docker. SENAITE Docker Container

Unciv. Open-source Android/Desktop remake of Civ V

karyoploteR. karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

metaflow. Build, Manage and Deploy AI/ML Systems

chromatiblock. Colinear block visualisation tool

Bacsort. a collection of scripts for organising bacterial genomes by species

corncob. Count Regression for Correlated Observations with the Beta-binomial

DAtest. Compare different differential abundance and expression methods

snakemake. This is the development home of the workflow management system Snakemake. For general information, see

dfast_core. DDBJ Fast Annotation and Submission Tool

cherchord. 🎸 Find chords for any string instrument quicky & easily 🎸

bionitio. Demonstrating best practices for bioinformatics command line tools

bionitio-python. Demonstrating best practices for bioinformatics command line tools

zotero. Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

ganon. ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

GrapeTree. GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

dehumanizer. rapidly rid reads of horrid humans

run_dbcan. Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

PythonPcl. Generating PCL, ZPL, etc directly with Python Code. /!\ Looking for Zebra Printer donation to work on this library /!\

getSeqENA. Get fastq files from ENA using Run IDs

SCARAP. A toolkit for prokaryotic comparative genomics

smudgeplot. Inference of ploidy and heterozygosity structure using whole genome sequencing data

PopPUNK. PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

FastDeMe. A fast, easy solution for metagenomic data analysis - Forked from Sander Vermeulens repository, developed during his internship

black. The uncompromising Python code formatter

olympus-photosync. This simple multi-platform application allows to download media through WIFI from digital Olympus cameras.

fastp. An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

public_kssd. K-mer substring space decomposition

KrakenTools. KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

BinSanity. Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation

IGGsearch. Metagenomic species profiling with enhanced coverage of the human gut microbiome

IGGdb. Database of genomes integrated from the gut microbiome and other environments

recentrifuge. Recentrifuge: robust comparative analysis and contamination removal for metagenomics

draftGenomes. Script to collect sequence files from multiple NCBI WGS projects and process them (LEGACY SOFTWARE)

fzf. :cherry_blossom: A command-line fuzzy finder

codi.vim. :notebook_with_decorative_cover: The interactive scratchpad for hackers.

BioD. A D library for computational biology and bioinformatics

metaWRAP. MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

figurefirst. A layout-first approach to figure making

labhandbooks. Information about what kinds of things people put in lab handbooks.

q. q - Run SQL directly on delimited files and multi-file sqlite databases