Questions tagged [khmer]

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9
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1answer
337 views

How to get the count of each kmer past 255 using khmer

I have a Fastq file and I want to get the exact count of each possible kmer from this file. On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
8
votes
2answers
9k views

How to use Python to count k-mers?

I have some FASTQ sequence files and a FASTA file for some regions I'm interested in. I would like: Build an index for the FASTA file Use the index to count number of k-mers occurred in my sequence ...