compressed meryl database to save space

[dgordon562]

I heard that there was a meryl 1.5 that allows compression. Is this true? Where can it be found? Will merqury work with it?

[arangrhie]

meryl v1.4.1 supports counting homopolymer compressed (hpc) kmers with compress. The rest of the operations work the same.
You can run Merqury on the hpc kmer db and uncompressed assemblies with -c option in Merqury.

Note the QV statistics are way off because the assumptions are different. Merqury generates spectra-cn plots and error kmer tracks, which are useful in very specific use cases, such as looking at hpc node sequences in Verkko graphs.

However, if the purpose is to evaluate the final assembly, I would not recommend to use the hpc kmers.

[dgordon562]

Thanks, Arang!
From your answer I'm going to assume:

1. there is no meryl 1.5 (Gemini hallucinating)
2. there is no compression (like gzip) of meryl databases that meryl can read

I tried to compress (tar/gzip) and then decompress when needed, but the resulting were not encouraging: for one meryl 1.4.1 14G database it took 22 minutes to compress, it took ~5 minutes to decompress and write it out, and it only yielded a 2:1 compression.

[arangrhie]

1. Yes there is no meryl v1.5 release, tell Gemini not to hallucinate! XD
2. Unfortunately no. I do gzip when needed, for archiving purpose or to share with collaborators.