Performance: multithreading delivers a 17x speedup, and new parallel GZIP compression makes v0.40 5x faster on I/O than v0.39. At 40 threads, a 78M read-pair plant dataset completes in ~11 min, on par with the highly optimised C++ tools.
New trimming steps: HEADCROP/TAILCROP for UMI & barcode removal, AVGQUAL for whole-read quality filtering, BASECOUNT for post-trimming length enforcement. Plus auto PHRED detection and built-in paired-end integrity validation.
Accuracy benchmark vs. fastp, RabbitTrim, BBDuk, Skewer & Cutadapt: Trimmomatic left only 14 residual adapter reads on the plant dataset. fastp: 810. Cutadapt: 23,874. And on the human dataset: 0. The palindrome algorithm still leads.
#OpenSource #Genomics
Marie Bolger closes the session at the #SOLRUB2025 with a presentation about the application of Helixer to the annotation of the #Solanaceae genomes.
Our paper on Trimmomatic v0.40 is officially published in Bioinformatics! A decade after the original, the ~50,000-times-cited NGS trimmer gets a major overhaul. Here's what's new 🧵
doi.org/10.1093/bioi...
#Bioinformatics #NGS
Today, a global community of hackers gathers in Berlin 🇩🇪 for the start of #BioHackEU25. Since 2019, over 2200 participants have gathered together for an intense week of collaboration to advance 275 projects.
Read the news: https://loom.ly/6sE_kdI
🎉Thank you all for joining #BioHackEU25! A special thanks to our online and overseas participants 🙌 staying up late hacking through different projects with us. 👏It has been a great week!! And we look forward to seeing you next year for #BioHackEU26 in Barcelona, Spain!🥳
The @denbi.bsky.social crew & friends from Germany at #BioHackEU25!
✨ We're halfway through #BioHackEU25!
This afternoon, all projects will present their 🎯 goals and challenges they’ve encountered and seek expertise from participants.
Keyword of this year: #Data, #Research, #FAIR and #Metadata
Hello, Bluesky! We’re AgBioData, a consortium of agricultural databases, researchers, and curators working to make genomic, genetic, and breeding data FAIR.
Follow us for updates on:
🔬 Data standards
📊 Tools & best practices
🌾 Community news
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#AgBio #OpenScience #FAIRdata #AgBioData
AbstractMotivation. Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its
