Bcool

de Bruijn graph cOrrectiOn from graph aLignment

Limasset A, Flot J-F, Peterlongo P (2020) Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 36:1374–1381

Dependencies

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.

Installation

git clone https://github.com/Malfoy/BCOOL/

./install.sh

For a faster install using 8 cores

./install.sh -t 8

Test

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.

Usage

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

Advanced options

Graph construction

-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)

Alignment

-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