MOTIVATION: Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution. RESULTS: We present the substantial updates to Trimmomatic over the past decade. Key enhancements include a robust multithreading model for high-performance parallel processing, parallel GZIP/BZIP2 compression, and a suite of new trimming and filtering steps to provide users with more flexible quality control. Usability has been significantly improved through automatic PHRED encoding detection and simplified file handling. The codebase has also been modernized including Maven support, and continuous integration to ensure long-term sustainability and community contributions. These updates solidify Trimmomatic's role as an efficient, flexible, and essential tool in modern bioinformatics pipelines. AVAILABILITY: Trimmomatic remains open-source under the GPL V3 license, with the latest version available at https://github.com/usadellab/Trimmomatic and also on our website https://www.plabipd.de/trimmomatic_main.html (DOI: https://doi.org/10.5281/zenodo.18678155).

This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

MOTIVATION: Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. RESULTS: We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. AVAILABILITY AND IMPLEMENTATION: MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. CONTACT: [email protected].