Comments (2)
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.
Related Issues (20)
- Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string HOT 5
- Compiling bcalm causes trouble when no .git repository is found HOT 1
- Output of bcalm2 similar to minia 3.2.1 unitigs? HOT 2
- Memory error with many reference genomes as input HOT 16
- High frequency of nodes with degree of two with length = 2k-1 HOT 2
- .fa files contain lowercase `km` instead of the documented uppercase `KM` HOT 3
- bcalm 2.2.1 on conda for Mac OS X produces incorrect cDBG (the zombie bug returns!!) HOT 12
- Add better input parsing HOT 1
- Improve error message for bad fasta input HOT 1
- Apparently bcalm crashes with very large k's (4096) HOT 1
- bcalm -version return code 1 to shell
- Glue is too strong, because glue files are not deleted.
- insert unitig disregarding the reverse complement HOT 1
- Option `-out-dir` is not used ? HOT 1
- bug report on a metagenomics dataset HOT 3
- Add header description with `-all-abundance-counts` HOT 2
- Is the output file reproducible? HOT 2
- Set the minimum value of -kmer-size HOT 1
- Counting kmers error HOT 2
- Fails to build from source on ARM MacOS HOT 1
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from bcalm.