de Bruijn CompAction in Low Memory

Possible use :

./bcalm input.dot

compact input.dot with l=10 in compacted.dot

./bcalm input.dot output.dot

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

./bcalm input.dot output.dot 8

compact input.dot with l=8 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 1110 for l=10 (ulimit -n 1100).

Each line in the input file is a distinct k-mer in lower-case, ending with a semi-column. Here is a sample input.dot:

actg;
ctga;
tgac;

You can convert DSK's output to bcalm's input as follows: use the parse_results program provided with DSK with the --dot flag, e.g.:

./parse_results dsk_output.solid_kmers_binary --dot > input_bcalm.dot

Each line is a simple path of the de Bruijn graph, in a similar format as the input.

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,
}