de Bruijn graph cOrrectiOn from graph aLignment
The installation script of Bcool compiles Bcalm2, Bgreat2, Btrim and ntCard.
This requires GCC>=4.9.1, CMAKE>=3.10, Autoconf, Automake and Python 3.
git clone https://github.com/Malfoy/BCOOL/
./install.sh
For a faster install using 8 cores
./install.sh -t 8
cd test
./test.sh
Bcool will be tested with a fixed kmer size and with ntCard
It should output
IT WORKS without ntcard !
and
IT WORKS with ntcard!
If only the first message is present, you can still use Bcool but you need to give a size of k to perform correction.
Standard command line
./Bcool.py -u reads.fa -o workingDirectory
With 20 cores
./Bcool.py -u reads.fa -o workingDirectory -t 20
With a fixed kmer size
./Bcool.py -u reads.fa -o workingDirectory -k 63
-s kmer filtering: kmer seen less than s time will not be included in the graph (default 2)
-S unitig filtering: unitig with abundance inferior to S will be removed from the graph prior correction (default 5)
-a anchor size: size of the seed of the alignment (default 41) lower value will increase sensibility and decrease throughput
-e mapping effort: number of different seed to test (default all) lower value will decrease sensibility and increase throughput
-m missmatches allowed: number of missmatches allowed for an alignment to be considered valid