SemiBin is a metagenomic binning tool (MAG builder). It is based on deep contrastive learning to incorporate background information (from reference genomes).

It achieves better results than other tools across a range of microbial habitats (both host-associated and environmental habitats).

Macrel (for metagenomic AMP classification and retrieval) is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes.

Its classifiers perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides. However, Macrel has a enhanced precision, recovering high-quality AMP candidates using real data.

NGLess is a domain-specific language for NGS (next-generation sequencing data) processing.

Jug is a light-weight, Python only, distributed computing framework.

Jug allows you to write code that is broken up into tasks and run different tasks on different processors. You can also think of it as a lightweight map-reduce type of system, although it's a bit more flexible (and less scalable).

It has two storage backends: One uses the filesystem to communicate between processes and works correctly over NFS, so you can coordinate processes on different machines. The other uses a redis database and all it needs is for different processes to be able to communicate with a common redis server.

Mahotas is a Python computer vision and image processing library. It includes many standard functions for image processing and feature computation and can be used to implement the approaches described in Coelho et al., 2013.

mahotas-imread is spin-off project which includes code to read/write images to files

argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) by CARD. It also provides drug categorization of drugs that antibiotic resistance genes confer resistance to.