Section: New Software and Platforms

MindTheGap

Keywords: Bioinformatics - NGS - Genome assembly

Functional Description: MindTheGap is a NGS software that performs local assembly of short reads. It is a structural variant detection tool as well as a genome assembly finishing tool. As a variant caller, it performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. It is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. Local assembly is performed to recover the inserted sequences from the whole read dataset. The local assembly module can also be used to fill the gaps between a set of input contigs without any a priori on their relative order and orientation, in order to improve a draft genome assembly.

Release Functional Description: Since version 2.1.0, MindTheGap can also be used as a genome assembly finishing tool: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. This new feature is available in the Fill module with option -contig.

• Participants: Claire Lemaitre, Guillaume Rizk, Pierre Marijon, Rayan Chikhi, Wesley Delage and Cervin Guyomar

• Contact: Claire Lemaitre

• Publication: MindTheGap: integrated detection and assembly of short and long insertions

• URL: https://gatb.inria.fr/software/mind-the-gap/