[khmer] Labeled de Bruijn graphs

[Guillaume Holley]

Dear khmer developers and users,

I am trying to use khmer to build the labeled de Bruijn graph of few 
hundreds bacterial strains represented as reads in FASTQ files. More 
precisely, I am trying to achieve the following tasks:

- Build the label de-bruijn graph.
- Query individual k-mers for their labels.
- Query individual k-mers for the number of successors and predecessors 
they have in the graph.

I spent some time reading the khmer documentation and the blog post 
http://ivory.idyll.org/blog/2015-wok-labelhash.html. Regarding this 
latter one, I have downloaded and installed the code to replicate the 
results but also read the code which gave me a first idea on how to 
achieved some tasks mentioned above.
However, I have few questions, maybe very naive since I am not very 
familiar with khmer.

- Is there any documentation for the API "labelhash"/"graphlabels"? I 
browsed the online documentation of khmer but could not find anything 
about it (maybe I just missed it). Do you know some examples different 
from the experiment mentioned in 
http://ivory.idyll.org/blog/2015-wok-labelhash.html ?

- I saw in the khmer v2.0 annoucement that "labelhash" was renamed 
"graphlabels". However I could not find anything in the khmer code about 
"graphlabels", only "labelhash", so should I continue using "labelhash"?

- the line "lh = khmer.LabelHash(args.ksize, args.tablesize, 
args.n_tables)" is used to build a labelhash, is there a way to specify 
we would like to build the graph from k-mers that occur a minimum of x 
times in their files ?

- In the example given on the blog to replicate the results, a labelhash 
graph is built from concatenated FASTx files. Is there a way to build 
the graph iteratively from FASTx files, without having to concatenate them ?

- I am currently working with k sizes bigger than 32, is there a way to 
work with khmer such that k > 32 ?

Thank your very much in advance for your time and help.

Best regards,

Guillaume Holley, PhD Student
Faculty of Technology, Genome Informatics group, Bielefeld University
Bielefeld, Germany