Compact representation of k-mer de Bruijn graphs for genome read assembly.

ABSTRACT:

Background

Processing of reads from high throughput sequencing is often done in terms of edges in the de Bruijn graph representing all k-mers from the reads. The memory requirements for storing all k-mers in a lookup table can be demanding, even after removal of read errors, but can be alleviated by using a memory efficient data structure.

Results

The FM-index, which is based on the Burrows-Wheeler transform, provides an efficient data structure providing a searchable index of all substrings from a set of strings, and is used to compactly represent full genomes for use in mapping reads to a genome: the memory required to store this is in the same order of magnitude as the strings themselves. However, reads from high throughput sequences mostly have high coverage and so conta

SUBMITTER: Rodland EA 

PROVIDER: S-EPMC4015147 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature