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A de novo genome assembler based on MapReduce and bi-directed de Bruijn graph | IEEE Conference Publication | IEEE Xplore

A de novo genome assembler based on MapReduce and bi-directed de Bruijn graph


Abstract:

The next generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. Assembly of NGS reads still...Show More

Abstract:

The next generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. Assembly of NGS reads still face great challenges due to the short reads and enormous high volume. In this paper, we presented a new assembler, called GAMR, which is based on bi-directed de Bruijn graph and implemented using MapReduce framework. We designed distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We evaluated GAMR using GAGE's data and compared it against other NGS assemblers. The results showed GAMR assembled contigs and scaffolds with better accuracy and longer N50 values.
Date of Conference: 15-18 December 2016
Date Added to IEEE Xplore: 19 January 2017
ISBN Information:
Conference Location: Shenzhen

References

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