KMC
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refresh-bio
Fast and frugal disk based k-mer counter
Hi, I am using kmc on fastq reads from sra archive and I hit into this issue. I found out that some reads in the fastq file are causing to...
I was looking at the is_allowed() method in mmer.h trying determine its purpose. The following line has a bug either in the code or the comment, not sure which. As...
Quick question / issue: Is it possible to update the counter for each kmer in the database to account for the sequencing depth of a particular experiment/FASTQ file?
Hi, I am trying to open a CKMCFile in listing mode and have it duplicated so that another CKMCFile object can continue reading from where the first one left off....
Add support for matching amino acid kmers. An amino acid kmer can be represented as a nucleotide kmer where each amino acid gets mapped to a canonical (e.g. lexicographically smallest)...
I would like to compare kmers from two nucleotide sequence fasta files but at the amino acid level, whereby DNA sequence --> peptide sequence --> kmer comparison at aa level...
As described at https://www.biorxiv.org/content/10.1101/179960v2 , extracting "skip-mers" (kmers that skip every 3rd base) can improve matching in coding regions. An option to extract such skip-mers rather than normal k-mers from...
Does KMC support the reading of crams? All my newest sequencing data is in cram format.
I using the latest kmc code but i can't count kmer on fastq file. It work on fasta ``` $cat r1_test.fq @0|Chromosome|4051100|4051286/2 BX:Z:CGACACGGTTTGGGCC AAACCCAACCAC + FFFFFFFFFFFF $kmc -fq -m5 -ci1...
Hi! This is not really an issue, but mostly a doubt. Since KMC can read BAMs, I wondered if this if for PacBio bams? I'll be anyway extracting fastas from...
