BCALM 2 is a bioinformatics software for constructing the de Bruijn graph of sequencing data.

More precisely, this repository is the new, parallel version of the BCALM software. It is using a new algorithm, and is implemented using the GATB library. The original, single-threaded code of BCALM (version 1) is still available at: https://github.com/Malfoy/bcalm

Read the instructions below to compile, then:

./bcalm -in [reads.fa] -k [kmer_size] -abundance [abundance_threshold]
./bglue -in unitigs.h5 -k [kmer_size]

e.g.

./bcalm -in reads.fa -k 21 -abundance 2
./bglue -in unitigs.h5 -k 21

GCC >= 4.8 or a very recent C++11 capable compiler

To retrieve bcalm and its submodule (gatb-core), type

git clone --recursive https://github.com/GATB/bcalm

For building your project, you should do the following

mkdir build;  cd build;  cmake ..;  make -j 8

Then, you should get a binary in

tools/bcalm

Note: the first compilation should take some time since the GATB-CORE library is generated.