Thanks @jianshu93. I suppose you would also suggest requiring FastANI 1.34 and using the -correct flag?

@AroneyS it seems the docs are wrong - https://wwood.github.io/CoverM/coverm-genome.html#dereplication-genome-clustering still talks about FastANI - can you make sure skani is being used by default and the docs reflect this please?

Hello @wwood,

Yes I would suggest so since the corrected flag is more close to the actual alignment-based ANI. We will update the bioconda channel for the newest --correct option soon.

Jianshu

hello @wwood pre-clustering default is now skani, which is very dangerous because below 82% ANI skani output is 0. I would suggest use finch version of minhash (essential the same with Mash without over-sketching) , above 90% ANI, skani is as good as fastANI, so I think it is ok to use. For pre-cluster, I would suggest use BinDash (https://github.com/zhaoxiaofei/bindash), I am developing bindash version 2 with Xiaofei. Bindash is as accurate as Mash but is 100 to 1000 times faster than Mash, dashing finch due to the theoretical breakthrough called B-bit one permutation MinHash with optimal/faster densification. BinDash can also be easily installed via bioconda. Theoretically, dashing has the largest variance, then Mash, BinDash has the smallest and it has the amazing property called locality sensitive hashing, neither above has this property. This idea is also implemented in my software called gsearch, for search and classification of genomes (will be published soon). See Gsearch here(https://gitlab.com/Jianshu_Zhao/gsearch), can be installed via bioconda. Let me know you what to also include gsearch into coverm, to classify genomes with extreme speed (almost in seconds).

Thanks,

Jianshu

Hi Team,

GSearch is out! It can search GTDB or entire Refseq/IMG_VR in almost no time! and the running time does not grow with increasing number of genomes! https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae609/7714450

I believe it will solve all the problems all other search and classification tools are having!

Thanks,

Jianshu