Section: New Software and Platforms

BCALM 2

Keywords: Bioinformatics - NGS - Genomics - Metagenomics - De Bruijn graphs

Scientific Description: BCALM 2 is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. It is a parallel algorithm that distributes the input based on a minimizer hashing technique, allowing for good balance of memory usage throughout its execution. It is able to compact very large datasets, such as spruce or pine genome raw reads in less than 2 days and 40 GB of memory on a single machine.

Functional Description: BCALM 2 is an open-source tool for dealing with DNA sequencing data. It constructs a compacted representation of the de Bruijn graph. Such a graph is useful for many types of analyses, i.e. de novo assembly, de novo variant detection, transcriptomics, etc. The software is written in C++ and makes extensive use of the GATB library.

• Participants: Antoine Limasset, Paul Medvedev and Rayan Chikhi

• Contact: Rayan Chikhi

• Publication: Compacting de Bruijn graphs from sequencing data quickly and in low memory

• URL: https://github.com/GATB/bcalm