Awesome

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,
}