KMC
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refresh-bio
Fast and frugal disk based k-mer counter
Hello, Thank you for developing kmc. I ran into an issue today before I realized I was using the wrong flag. When using -fa instead of -fm, kmc (v3.2.1) runs...
Hi, Is there a way to dump the `canonical minimizers` or `superKmers` without having to reach the final stage? I have read the API docs but didn't find an exposed...
Dear Sir, I saw kmc_genome_counts is used in https://github.com/msauria/T2T_Kmer_Analysis for the analysis of the T2T genome. But I cannot find it in the current KMC. I wonder how I would...
Hi, I want a count table (m× n) like this: |# kmer seq | sample1 |sample2 | ...| |---|---|---|---| |AAA...|1|2|...| |AAC...|0|5|...| |AAG...|4|2|...| where m is number of samples or individuals...
Hi, first of all, thanks for the tool, it is indeed pretty fast and efficient! I wanted to ask you how to achieve the following: I have `N` genomes (assembly)....
I want to assess my assembly genomes. So I run the kmc count (ci0) with illumina_reads and assembly genomes and get two kmc database indepedently. Then I use KMC_tools analyze...
hello I am confusion with the command for the kmc count kmer with assembly genome (fasta). I actually do not find an example. My command is kmc -k21 -ci0 -t40...
installing with conda install kmc does give segementation fault when runnin kmc. conda install -c bioconda/label/cf201901 kmc works
When filtering reads, if the reads are paired, it would help to be able to say either "keep both reads if one passes the filter" or "drop both reads if...
Add to kmc_tools a command that prints (in either human- or machine-readable form) information about a kmer database: kmer size, single-/double- strandedness, number of kmers in the database.