Bracken is the recommended post-processer of Kraken2 outputs and specifically is expected to improve relative abundance estimates. However, Bracken's Github has over 100 outstanding issues and the code seems to rely on Python 2, which is outdated. While many of the github issues are likely not due to bugs, it does seem like the software does not seem to be supported strongly at this time. I am curious what other alternatives exist. Are folks moving from kraken2/bracken to another solution for quick taxonomic hypothesis generation of metagenomics data?
No, Braken is the tour de force of first stage post-hoc Kraken2 analysis.
Whether the code is supported or not it corrects bias in Kraken2 population frequency distributions. I'm not aware of any theoretical concerns.
Generally, Python2 isn't a good idea, but it is overshadowed with the bigger concern of population bias, which is what Braken is there to adjust.