KMC
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refresh-bio
Fast and frugal disk based k-mer counter
Hi, Say that I have a fasta file with 10 reads, Is there a way to tell KMC to generate different kmer count output for each one of the reads...
Can KMC count kmers for the protein sequences instead of nucleotides? Thanks
Hi, I'm using kmc_tools to reduce, intersect, etc. KMC2.x databases. `reduce` converts my KMC2.x database to a KMC1.x database and I was wondering whether there is a way to convert...
Hi, I am trying to use complex command to find the union of bunch of kmer counts. However, some kmers do not show in my final output file. For example,...
I'm trying to do kmer counting on some GIAB fastq.gz files which have reads of varying length. However, when I try to run KMC I receive the very vague error...
[GCF_000392535.3_ASM39253v3_genomic.fna.gz](https://github.com/refresh-bio/KMC/files/2127232/GCF_000392535.3_ASM39253v3_genomic.fna.gz) For this test_data, which is downloaded from ncbi, we can use kmc (./kmc -k18 -ci1 -cs1 -fm -f filename outputname ./tmp_data) to generate .pre and .suf files, and then...
@marekkokot It would be great if you could support gapped kmers. The only change is in extracting kmers from reads. E.g. for 4-mers with a 2-base gap in the middle,...
Add option to create a kmer database from a simple text file listing the kmers and their counts, like what kmc_tools transform dump outputs. If counts are omitted, set them...
Add option to keep only reads containing a stretch of M _adjacent_ kmers at least N of which are in the database. This permits more flexible filtering than just using...