https://github.com/Malfoy/BCALM
Tip revision: 07c86e0dccb6ea271d530c1f66e3483c31ddc935 authored by Malfoy on 15 January 2016, 15:32:36 UTC
Update README.md
Update README.md
Tip revision: 07c86e0
README.md
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,
}