BLESS 2

Accurate, memory-efficient and fast error correction method

Yun Heo, Anand Ramachandran, Wen-Mei W Hwu, Jian Ma, Deming Chen

Research output: Contribution to journalArticle

Abstract

The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes. Availability and implementation: Freely available at https://sourceforge.net/projects/bless-ec.

Original languageEnglish (US)
Pages (from-to)2369-2371
Number of pages3
JournalBioinformatics
Volume32
Issue number15
DOIs
StatePublished - Aug 1 2016

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Error correction
Error Correction
Data storage equipment
Genome
Efficiency
Genes
OpenMP
Vertex of a graph
Sequencing
Availability
Programming
Computing

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

BLESS 2 : Accurate, memory-efficient and fast error correction method. / Heo, Yun; Ramachandran, Anand; Hwu, Wen-Mei W; Ma, Jian; Chen, Deming.

In: Bioinformatics, Vol. 32, No. 15, 01.08.2016, p. 2369-2371.

Research output: Contribution to journalArticle

Heo, Yun ; Ramachandran, Anand ; Hwu, Wen-Mei W ; Ma, Jian ; Chen, Deming. / BLESS 2 : Accurate, memory-efficient and fast error correction method. In: Bioinformatics. 2016 ; Vol. 32, No. 15. pp. 2369-2371.
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