An Efficient DBG Indexing Method for Large-Scale Read Mapping

doi:10.12068/j.issn.1005-3026.2023.06.002

Abstract

Abstract: In order to answer two questions about de Bruijn graph(DBG) in bioinformatics: ① For any k-mer， answer whether it is the vertex of DBG; ② For any vertex of DBG， answer its adjacency information(incoming edge and outgoing edge)， an efficient DBG indexing method for large-scale read mapping is proposed. In this paper， the above two questions are transformed into the exact finding problem of k-mer and (k+1)-mer on non-repetitive multipath， and are solved by using FM-index. Firstly， a given reference sequence is compressed， which is the discovery of non-repetitive multipaths， thereby compressing the presence of large-scale repetitive (k+1)-mers in the sequence. Secondly， the DBG is indexed based on the non-repetitive multipath FM-index. The k-mer is searched whether it appears on the DBG， and if so， the direct predecessor and direct successor nodes of the k-mer are provided to improve the spatial-temporal efficiency. Finally， experiments are performed on the genomes of 62 E. coli strains. The experimental results show that the method proposed can efficiently index the DBG of multi-reference sequences.

Key words: de Bruijn graph; index; read mapping; FM-index; reference sequence

CLC Number:

TP274

YU Chang-yong， LI Jun-jie， MA Hai-tao， ZHAO Yu-hai. An Efficient DBG Indexing Method for Large-Scale Read Mapping[J]. Journal of Northeastern University(Natural Science), 2023, 44(6): 770-776.

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