A novel approach to full-length 16S rRNA gene reconstruction from short read data
METASEED uses the amplicons and shotgun metagenome reads. The utilization of this data helps our pipeline to determine original 16S regions. A key step in METASEED is the uniqueness criteria, where the seed (amplicon sequences) and metagenome reads are uniquely matched depending on their abundance. The novelty of METASEED pipeline resides in our own optimized criteria that eliminate undesirable noises and produce high quality, reasonable length 16S sequences. The method is designed to broaden the repertoire of sequences in 16S rRNA reference databases by reconstructing novel near full length sequences.
If you want to test the METASEED method, you can download this tar-archive, untar it, and read its README.html on how to run the procedure on the small sample data set provided: (https://arken.nmbu.no/~pmelcy/share/METASEED/METASEED.tar.gz)
Philip, M., Rudi, K., Ormaasen, I. et al. METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data. BMC Bioinformatics 25, 237 (2024). https://doi.org/10.1186/s12859-024-05837-z