Note : BCALM2 is available at https://github.com/GATB/bcalm

bcalm
=====

de Bruijn CompAction in Low Memory

Possible use :

    ./bcalm input
compact input with l=8 in compacted.dot

    ./bcalm input output.dot
compact input with l=8 in output.dot

    ./bcalm input output.dot 10
compact input with l=10 in output.dot



Nota Bene :   
Higher l mean lower memory but the algorithm will NOT work with l>10.   
Also note that to use l>=8 you have to allow 260 open files (type `ulimit -n 260` in a terminal)
and 1100 for l=10 (`ulimit -n 1100`).

Input
=====

Each line in the input file is a distinct k-mer in upper-case, ending with his counting (not required). Here is a sample input:

AATCGATCG 3
ATCGATCGT 33
TCGATCGTA 645

It is the typical ouput of DSK with the dsk2ascii script (see http://minia.genouest.org/dsk/)

Output
=====

Each line is a simple path of the de Bruijn graph, in lowercase. Here is a sample output:

aatcgatcgta;


License
=======

BCALM's license is BSD with Attribution. In informal words, any use is permitted as long as it acknowledges us. For example with a citation to:

    @inproceedings{reprdbg14,
    author = {Chikhi, R. and Limasset, A. and Jackman, S. and Simpson, J. and Medvedev, P.},
    title = {{On the representation of de Bruijn graphs}},
    booktitle = {RECOMB},
    publisher = {Springer},
    year = 2014,
    }