Name
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. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1109/BIBM.2016.7822494 | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) |
Keywords | Field | DocType |
next generation sequencing (NGS),assembly,MapReduce,bi-directed de Bruijn graph | Genome,Computer science,Theoretical computer science,Genomics,Contig,Distributed algorithm,De Bruijn graph,DNA sequencing,Bioinformatics,Scalability | Conference |
ISSN | ISBN | Citations |
2156-1125 | 978-1-5090-1612-9 | 0 |
PageRank | References | Authors |
0.34 | 5 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Yuehua Zhang | 1 | 0 | 0.34 |
| Pengfei Xuan | 2 | 16 | 3.07 |
| Yunsheng Wang | 3 | 1 | 1.04 |
| Pradip K. Srimani | 4 | 879 | 96.11 |
| Feng Luo | 5 | 284 | 26.03 |