Comments (3)
The latest release candidate (canu branch 1.9) or this version of meryl should both have beryl-lookup which replaces simple-dump. It will give you info on the kmers from a db in a fasta file.
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meryl-lookup -existence
gives you the number of kmers intersected in both your sequence fasta file and haplotype specific kmer db. Sorry for the confusion with the uncomplete codes. Will try update my script when I get more time.
from meryl.
Hey that's great- I'm just grateful to see the k-mer dump is implemented here! Overall this version of meryl is more intuitive to me than before. I ran meryl-lookup on a small dataset this morning with success using this branch, thanks!
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Related Issues (20)
- Homopolymer compression is not applied if the first read file is empty HOT 1
- compile problem HOT 2
- How to cite meryl? HOT 4
- meryl terminates with 'std::bad_alloc' and failed assertion HOT 3
- [Compile] ‘gettimeofday’ was not declared in this scope HOT 1
- bitArray-v1.H:86 problem when running the pipeline HOT 1
- Compile error HOT 2
- feature request: filter reads with kmers from bam file? HOT 5
- the parental specific kmers were intersected in progeny genome HOT 2
- How do you plot? HOT 3
- version question about meryl HOT 1
- Conda version issues
- meryl count assertion failed with large K HOT 1
- How to install meryl2? HOT 1
- API docs HOT 1
- Use sequence to query meryl db HOT 1
- Is this output correct? HOT 2
- Run Meryl on multiple fastq files HOT 2
- How to get kmer count in query fastq files with kmer database HOT 2
- conda install may have broken (possibly with a recent update?) HOT 1
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