Software

I have written some open-source software, some to scratch an itch, and some as part of my research.

Currently Active Projects

SemiBin

SemiBin is a metagenomic binning tool which uses self-supervised deep learning to reconstruct genomes (MAGs) from short- and long-read data.

More information: https://semibin.rtfd.io

License: MIT.

Macrel

Macrel screens genomes and metagenomes for antimicrobial peptides: https://github.com/BigDataBiology/macrel

Described in MACREL: antimicrobial peptide screening in genomes and metagenomes (PeerJ, 2020).

argNorm

argNorm normalizes the output of antibiotic resistance gene annotation tools to the Antibiotic Resistance Ontology (ARO), so that results from different tools can be compared: https://github.com/BigDataBiology/argNorm

Described in argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) (Bioinformatics, 2025).

License: MIT.

NGLess

NGLess is a domain specific language for Next-Generation Sequencing (NGS) processing, with a focus on metagenomics.

More information: https://www.big-data-biology.org/software/ngless/

License: MIT.

mahotas

mahotas is a computer vision package for Python. It operates on numpy arrays. It is implemented in C++ as it has a strong efficiency focus.

License: MIT.

Jug

Jug is a task based framework for running embarrassingly parallel code in Python. You can also think of it as a light-weight python-based map-reduce environment.

License: MIT.

mahotas-imread

Imread serves to read and save image files to and from numpy arrays.

License: MIT.

conduit-algorithms

A series of conduit based algorithms in Haskell.

License: MIT

Diskhash

Disk-based hashtable: https://github.com/luispedro/diskhash

fasta_reader

Uses diskhash to index a FASTA file making it very fast to retrieve a sequence:

https://github.com/luispedro/fasta_reader

Data Resources

Large datasets produced by the lab, browsable online:

  • AMPSphere: a catalogue of candidate antimicrobial peptides from the global microbiome (paper).
  • GMSC: the Global Microbial smORF Catalogue, of small proteins (paper).
  • GMGC: the Global Microbial Gene Catalog (paper).

Reproducible Research

I have also made some code available for reproducible research of published papers.

Dormant Projects

These are projects that work but which I am not too interested in pursuing right now, but which I might revive in the future.

Pymorph: Python Morphology Toolbox

This is a Python image morphology toolbox which I have adopted (i.e., taken over maintaining). This works, but I am not adding any more functionality.

Includes basic operations such as

  • erode
  • dilate
  • open
  • tophat opening
  • watershed
  • ...

License: BSD.

Hex

Hex is a TeX engine in Haskell. It currently does not do much, but it is progressing. The goal is a full reimplementation.

License: GPL.