Hi there,
I recently reconstructed or identified some 16S genes using tools like MATAM or barrnap, respectively. I noticed the resulting fragments of 16S gene varied across samples or MAGs, generally with a divergent length of 300~1500 bp. My aim is to find if there is any novel lineage of high rank in my samples, however, with a low computation cost, which renders me not to directly analyse MAGs.
To my current knowledge, the 16S phylogenetic analysis is commonly based on one or two of all the hypervariable regions, using the virtually same long fragments. That doesn't suit to my fragments.
I also learned some tools conduct de novo taxonomy, such as AutoTax. However, full length 16S is required. I am not sure whether this sort of method is also applicable to non full length 16S.
How can I deal with my fragements to perform phylogenetic analysis? My current plan is to discarded those short fragments which mostly derived from 16S identification in MAGs, and retain near full-length fragments (>1400 bp, or best 1500 bp).
Many thanks in advance.