other k mer resources

Software

K-mer counters

• KMC: a faster and versatile k-mer counter
• KAT: k-mer counting and comparison tool, capable of comparing multiple libraries.
• khmer: probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization.
• Jellyfish: very easy to operate, but certainly not the fastest k-mer counter out there
• FASTK: Presumably the fastest counter, but it is unable to count repetitive kmers; using a workaround and modified version of genomescope called Genomescope.FK the genome size estimates are still in the right ballpark.

Kmer spectra analysis tools

• GenomeScope - a kmer spectra analysis tool suited for polyploids as well
• tetramer - fitting pamaters to k-mer spectra of allotetraploids
• findGSE - an alternative model for fitting genome sizes

QC of genome assembly

• KAT - KAT can plot the k-mer spectra with colouring by the frequency of the given k-mer in assembly, which is a very smart way how to inspect collapses of paralogs and duplicates.
• Merqury - Just like KAT but also made for trio data and coloring the assembly by the maternal and paternal contribution

Learning materials

General

• Rob Edwards' video introduction to concept of k-mers
  • it's mostly in the context of genome assembly
• Bernardo Clavijo's introduction to k-mer counting

Taxonomy

• A post about k-mers - this time for taxonomy!
  • partially based on k-mers and sourmash