Any opinions on the use of (or experience with) BWBBLE?

Question

[kirannbishwa01]

Would someone be able to share their opinion on the use of BWBBLE? https://github.com/viq854/bwbble

I am not asking how to use it, but if you have used it what is your experience and opinion:

• Would it be a good choice compared to other aligner to increase alignment hits?
• Does it promote or attract more paralogous alignment due to more matches allowed?
• Can it be handled by GATK engine or other tools to do downstream variants (SNPs, InDels, etc calling)?
• Variant qualities?
• Phasing possibilities and compatibility with other tools?
• Other suggestions?

I can do all this on my own but I don't want to be spending another month trying to figure this all out. Please be kind to share your experience.

[h.mon]

Based on a quick look at NCBI's BWBBLE papers citations (8, no one really using it), I think you will have to do the comparisons on your own. Have a look at this blog post, though no comparisons here as well.