Introduction

kMer provides a command-line analysis toolkit for creating, analysing, and manipulating k-mer profiles. It is implemented in Python.

After following Installation, kMer can be started by typing:

$ kMer

More information about the available commands and their arguments is printed by adding the -h argument.

For example, to count all 9-mers in a FASTA file, use the count command:

$ kMer count -k 9 example.fasta example.k9

Below, we provide an overview of all functions of kMer that are available via the command-line interface:

Command	Description
count	Make a profile from a FASTA file.
merge	Merge two profiles.
balance	Balance a profile on the frequency of k-mers and their reverse complements.
showbalance	Calculate the balance of a profile.
meanstd	Show the mean and standard deviation of k-mer frequencies.
distr	Calculate the distribution of the frequencies in a profile.
info	Print basic statistics on a given profile.
getcount	Retrieve the count for a particular k-mer.
positive	Only keep counts that are positive in both profiles.
scale	Scale profiles such that the total number of k-mer frequencies is equal.
shrink	Shrink a profile, effectively reducing k-mer length.
shuffle	Randomise a profile.
smooth	Smooth two profiles by collapsing sub-profiles.
distance	Calculate the distance between two profiles.
matrix	Make a pairwise distance matrix for a series of k-mer profiles.

More information about the methods implemented by kMer can be found in Methodology. Some examples of working with the toolkit are shown in Tutorial.