MindTheGap: integrated detection and assembly of short and long insertions.

ABSTRACT:

Motivation

Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants.

Results

We propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MindTheGap uses an efficient k-mer-based method to detect insertion sites in a reference genome, an

SUBMITTER: Rizk G 

PROVIDER: S-EPMC4253827 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature