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Extreme-Scale De Novo Genome Assembly

Journal Article ·
DOI:https://doi.org/10.1201/b21930· OSTI ID:1398520
 [1];  [2];  [3];  [2];  [2];  [3];  [2]
  1. Intel Corporation, Santa Clara, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division
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De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and the large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1398520
Country of Publication:
United States
Language:
English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES