A very short newsletter to announce the release of the new FROGS article entitled "FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers", which you can read here : https://academic.oup.com/bib/advance-article/doi/10.1093bib/bbab318/6354026?guestAccessKey=c3c28079-333a-432e-9d9e-b4c37da8284d.
For the analysis of fungal communities, the region commonly targeted is the ITS (Internal Transcribed Spacers). These sequences have the particularity of being variable in size depending on the organism and the long ITS are then excluded by bioinformatics analysis methods. FROGS has taken these particularities into account throughout the analysis process, and thus makes it possible to analyze fungal communities by command line or through an easy-to-use web interface. These innovations of FROGS dedicated to long reads have been compared to those of other popular tools (DADA2, QIIME2, USEARCH) and described in this article. Compared to other methods, FROGS produces very few false positives and false negatives, has an excellent recall rate and high precision. This strategy can also be used for any non-contiguous amplicon such as D1-D2 and rpb2.
Enjoy reading it! Géraldine, Maria & Olivier.