reapxdev/zenodo-scraper huggingface dataset:
The state of M. tuberculosis tooling in bio.tools — a registry audit
Authors: Sharma, Abhinav
Type: Software
Published: 2026-08-02
Keywords: bio.tools, Mycobacterium tuberculosis, research software sustainability, link rot, bioinformatics registries

A reproducible audit of how M. tuberculosis and mycobacterial bioinformatics software is represented in the bio.tools registry: corpus size, declared tool types, homepage reachability, and version/licence completeness. Finds that registered mycobacterial tooling is a small fraction of the genomics corpus, that it is disproportionately built as hosted resources rather than installable artefacts, and that homepage decay falls entirely on the hosted class.
Analysis scripts for genome-wide reverse-ORF discovery in metapneumoviruses
Authors: Bartas, Martin, Červeň, Jiří, Volná, Adriana
Type: Software
Published: 2026-08-02
Keywords: metapneumovirus, human metapneumovirus, avian metapneumovirus, reverse open reading frame, rORF, negative-sense RNA virus, viral genomics, comparative genomics, ORF discovery, ambigrammatic genome

<p>This software package contains eight standalone Python scripts developed for genome-scale analysis of reverse open reading frames (rORFs) in metapneumovirus genomes. The scripts implement genome-wide rORF discovery, composition-preserving nucleotide shuffling, gene-resolved codon-aware controls, hotspot mapping, P-AS1/F-AS1 amino-acid conservation and divergence analysis, Kozak-context screening, screening for HMPV-like gene-start and gene-end signals, and exploratory analysis of the upstream-AUG architecture of F-AS1. A README describes the required inputs, dependencies, command-line usage, and expected outputs. Sequence and alignment inputs are provided separately as Supplementary Data accompanying the related manuscript. The software is released under the MIT License.</p>