Section: New Software and Platforms

MindTheGap

Keywords: Bioinformatics - NGS - Genome assembling

Functional Description

MindTheGap 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. The main algorithmic improvement of version 2.0.0 is to detect additionnal variants, such as SNPs and deletions. This feature improves the sensitivity of the insertion detection algorithm for insertions that are located near these other variants. Additionnally, MindTheGap performs de novo assembly using the de Bruijn graph implementation of GATB. Hence, the computational resources required to run MindTheGap are significantly lower than that of other assemblers.

• Participants: Claire Lemaitre and Guillaume Rizk

• Contact: Claire Lemaitre

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