BinDash 2.0 usage and build?

[jdwinkler]

Thanks for your work on BinDash! I am interested in using BinDash2.0 as a replacement for Mash. Is there a particular commit I should build to try it? If it is possible for you to provide an example of the output format, that would be great as well.

Thank you in advance!

[jianshu93]

Hi @jdwinkler,

You can use the bioconda version if you do not want to build from source. But this repo is the most recent version and is consistent with the bioconda version. Output format is exact the same with Mash, commands would be like:

### strep_small_name.txt is the query genome path (gz supported), sketch 188*64=12032, to be accurate at > 99.99% ANI
bindash sketch --kmerlen=16 --nthreads=32 --sketchsize64=188 --dens=2 --bbits=32 --minhashtype=2 --listfname=strep_small_name.txt --outfname=strep_small_k16_s500.bindash

### database_name.txt is the database genome path (gz supported)
bindash sketch --kmerlen=16 --nthreads=32 --sketchsize64=188 --dens=2 --bbits=32 --minhashtype=2 --listfname=database_name.txt --outfname=database.bindash

bindash dist --nthreads32 --outfname=S_bindash_new.txt strep_small_k16_s500.bindash database.bindash

Thank you for your interest in BinDash 1/2.

Jianshu & Xiaofei

[jdwinkler]

Thank you!