AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality

U Rashid, C Wu, J Shiller, K Smith, R Crowhurst… - …, 2024 - academic.oup.com
Genome assembly projects have grown exponentially due to breakthroughs in sequencing
technologies and assembly algorithms. Evaluating the quality of genome assemblies is …

SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline

S Potente, D Boscarino, D Paladin… - Briefings in …, 2025 - academic.oup.com
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy
number alterations (CNAs). However, there remains a gap for a standardized workflow …

BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization

G Marchment, B Brancotte, M Schmit… - NAR Genomics and …, 2024 - academic.oup.com
Bioinformatics workflows are increasingly used for sharing analyses, serving as a
cornerstone for enhancing the reproducibility and shareability of bioinformatics analyses. In …

Artificial Intelligence to Reshape the Healthcare Ecosystem.

G Reali, M Femminella - Future Internet, 2024 - search.ebscohost.com
This paper intends to provide the reader with an overview of the main processes that are
introducing artificial intelligence (AI) into healthcare services. The first part is organized …

Improving the Reliability and Quality of Nextflow Pipelines with nf-test

L Forer, S Schönherr - bioRxiv, 2024 - biorxiv.org
The workflow management system Nextflow builds together with the nf-core community an
essential ecosystem in Bioinformatics. However, ensuring the correctness and reliability of …

Cloudgene 3: Transforming Nextflow Pipelines into Powerful Web Services

L Forer, S Schönherr - bioRxiv, 2024 - biorxiv.org
Nextflow has emerged as a flexible and scalable workflow system for building computational
pipelines in life sciences. Simultaneously, Software-as-a-Service platforms enable …