I have sequenced a bacterial genome with Illumina 2x300 pb kit and after that I have assembled the genome using SPADES (and also A5 pipeline).
The problem is that the draft genome does not present a full 1500 pb rRNA 16S gene. It is expected, since assemblers do not do a great deal with repetitive regions.
However, I need the full-length 16S rRNA gene for my research purposes (taxonomy). Is that a way to recover it from the genome reads (>30 x coverage)?
PS: I have found a promising program named Reago, but it did not worked for me. It seems it does not deal with reads over 101 bp.