Can I submit a subset of kmers from the reads? about bcalm HOT 2 OPEN

By the way, thanks for the algorithm and tool. It is very elegant.

from bcalm.

Hi Richard, and thanks for the kind words!

For now, you can specify a minimum/maximum kmer abundance threshold using the options -abundance-min A -abundance-max B, noting that it will keep only kmers of abundance A<=x<=B.

Otherwise, the input formats of Bcalm are fasta/fastq reads, or a custom HDF5 file that contains counted k-mers. That format isn't that easy to create from scratch, but not impossible for us to maybe write a custom program for that. In that format, Bcalm expects that kmers are partitioned according to their minimizer.

Giving as input a fasta file with one kmer per sequence would be an acceptable solution, bearing in mind that abundance would be lost (unless the kmer is repeated as many times as its abundance, which isn't very elegant).

What's the volume of kmers that you wish to give to Bcalm: 10's of millions, billions?
Also, in what format do you have the counted k-mers right now?

from bcalm.