Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.

ABSTRACT:

Background

High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome. It can be transformed into a set of sequences "colored" by the genomes to which they belong. A colored de Bruijn graph (C-DBG) extracts from the sequences all colored k-mers, strings of length k, and stores them in vertices.

Results

In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the bloom filter trie (BFT). The data structure allows to store and compres

SUBMITTER: Holley G 

PROVIDER: S-EPMC4832552 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature