khmer_uniquekmers

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. Adapted from nf-core/modules khmer/uniquekhmers.

khmer
k-mer
effective genome size
nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install khmer/uniquekmers

https://github.com/CCBR/nf-modules/…/modules/CCBR/khmer/uniquekmers/

Input

name type description pattern
fasta file fasta file *.{fa,fasta}
kmer_size integer k-mer size to use [0-9]+

Output

name type description pattern
report file Text file containing unique-kmers.py execution report report.txt
kmers file Text file containing number of kmers kmers.txt
versions file File containing software versions versions.yml

Tools

khmer

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khmer k-mer counting library