2026· Methods in molecular biology· Vol 3017, pp.
39-46
· 0 citations
Medicine
TL;DR
FASTA-Fetcher is described, a free, cross-platform, GUI-based application that automates large-scale sequence acquisition using NCBI accession numbers and empowers researchers and students to incorporate high-throughput molecular workflows into their studies with confidence and ease.
An open, interactive and web-based tutorial that guides scholars with basic command-line skills through the detailed development of a validated and reproducible Nextflow metagenomics classification pipeline, which aims to lower technical barriers in microbiome bioinformatics and promote best practices in metagenomics d...
This study presents the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes, highlighting tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin.
Mateusz Jundzill, Martin Hölzer, S. Mangul et al.· Genome Biology· 0 citations
Prokanota provides an accessible and reproducible annotation backbone while allowing project-specific databases and evidence layers to be incorporated without modifying workflow code, and fills a practical gap between fixed, standardized annotation tools and fully custom expert-built workflows.
Richard Stöckl, Felix Grünberger, Dina Grohmann· F1000Research· 0 citations
Rapid and accurate microbial identification is critical for interpreting biological data in basic research and when making applied decisions on how to effectively treat patients and control human, animal, and plant diseases. Advancements in high-throughput sequencing have the potential to expedite fungal species identi...
Hayden Johnson, B. Vinatzer, R. Mazloom et al.· bioRxiv· 0 citations
PyiTOL validates inputs, generates 31 iTOL template schemas, performs LCA-based monophyly classification with nested-monophyly detection, sampling-completeness states and polyphyletic subgroup decomposition, plus API upload and session replay.
Zi-Chao Zeng, Yin-Zhao Wang· bioRxiv· 0 citations
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