pbelmann

SteadierCom

Microbial community simulation

horovod

Distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.

fcs

Foreign Contamination Screening caller scripts and documentation

snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

genomad

geNomad: Identification of mobile genetic elements

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

memusg

A 'time'-like utility for Unix that measures peak memory usage

oscar

Open Source Serverless Computing for Data-Processing Applications

KEMET

KEGG Module Evaluation Tool

IGGdb

Database of genomes integrated from the gut microbiome and other environments

pachyderm

Data-Centric Pipelines and Data Versioning

Diamond

Diamond is a python daemon that collects system metrics and publishes them to Graphite (and others). It is capable of collecting cpu, memory, network, i/o, load and disk metrics. Additionally, it features an API for implementing custom collectors for gathering metrics from almost any source.

shell

Pop!_OS Shell

bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

llm-course

Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

nextflow-spark

CheckM2

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

autoscaling-cluster

PySnooper

Never use print for debugging again

Hands-On-Graph-Neural-Networks-Using-Python

Hands-On Graph Neural Networks Using Python, published by Packt

nf-validation

Params validation plugin for Nextflow pipelines

nf-test

Simple test framework for Nextflow pipelines

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.

age

Graph database optimized for fast analysis and real-time data processing. It is provided as an extension to PostgreSQL.

UniqueKMER

Generate unique KMERs for every contig in a FASTA file

DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Spring

FASTQ compression

fastq_compression_comparison

Creating a simple Docker image to help perform comparisons for FASTQ compression

BacArena

agent based modelling