KMC
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Fast and frugal disk based k-mer counter
It'd be great to add an option to store for each kmer, instead of its count, the minimum or maximum position of that kmer in the input sequences. This would...
It's great that kmc now supports bam files input. Could you extend that to filtering reads? (For input and output).
Currently, a kmer that occurs twice in the same read gets a count of 2, same as a kmer that occurs once in two different reads. But the latter kmer...
Dear developers of KMC, It would be great if there was an independent interface for building KMC database similarly to reading implemented in kmc_api/kmc_file. - [ ] API for counting...
Sometimes a kmer might appear in different reads, so it looks real, but all these reads are duplicates. It would be good if there was an option to drop kmers...
When a kmer in a read includes IUPAC ambiguity codes, add all possible concretizations of that kmer.
Currenlty ```kmc``` (except for small k) and ```kmc_tools``` store counters of kmers on uint32_t, which is reasonable for k-mer counters, but the counter field in kmc_database may be also used...
The output file format for filtering of reads is said to default to "same as input". But if the input is myfile.fasta.gz , the output is uncompressed even if named...