IntroductionΒΆ
kPAL provides a command-line analysis toolkit for creating, analysing, and manipulating k-mer profiles. It is implemented in Python.
After following Installation, kPAL can be started by typing:
$ kpal
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:
$ kpal count -k 9 example.fasta example.k9
Below, we provide an overview of all functions of kPAL 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. |
cat | Save profiles from several files to one file. |
More information about the methods implemented by kPAL can be found in Methodology. Some examples of working with the toolkit are shown in Tutorial.