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airdna_pilot

amazon-urbanization

annotapipeline

Genome annotation pipeline

arrival-movie-live-coding

Documents from a live coding session by Christopher Wolfram related to content from the 2016 film Arrival

awesome-fair

A curated list of awesome stuff around the FAIR principles for (scientific) data, i.e that data is findable, accessable, interoperable and re-usable.

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

bgcflow

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

boss-runs

Dynamic, adaptive sampling during nanopore sequencing

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

cap2

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

earthnetwork

Microbial co-occurrence network inferred from Earth Microbiome Project

emp

Code repository of the Earth Microbiome Project.

essential-math-for-ai

This repository contains the supplementary material associated with my book: Essential Math for AI published by O'Reilly Media

eukdetect

eukheist

funcscan

(Meta-)genome screening for functional and natural product gene sequences

fungaltraits

A dynamic database of fungal trait measurements

funguild

FUNGuild: parsing OTUs into functional guilds

genomics-in-azure-code

Companion code repository for the "Genomics in the Azure Cloud" book

gpu-jupyter

GPU-Jupyter: Leverage the flexibility of Jupyterlab through the power of your NVIDIA GPU to run your code from Tensorflow and Pytorch in collaborative notebooks on the GPU.

insect-detect

Detection models and Python scripts for automated insect monitoring with the Insect Detect DIY camera trap.

lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.

markermag

Linking MAGs with 16S rRNA marker genes

metaeuk

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

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

metasub_cap

A comprehensive pipeline for short read metagenomic data

micom

Python package to study microbial communities using metabolic modeling.

mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

nanoseq

Nanopore demultiplexing, QC and alignment pipeline