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BLESS | Bloom filter-based error correction solution for high-throughput sequencing reads

A memory-efficient error correction method that uses a Bloom filter as the main data structure. 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 percent higher gain while retaining the memory efficiency of the previous version for large genomes.

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BLESS classification

BLESS specifications

Unique identifier:
OMICS_02246
Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Parallelization:
MPI, OpenMP
Computer skills:
Advanced
Stability:
Stable
Name:
BLoom-filter-based Error correction Solution for high-throughput Sequencing reads
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
C++
License:
GNU General Public License version 3.0
Version:
2.0
Maintained:
Yes

BLESS distribution

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BLESS support

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Publications

Institution(s)

Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA

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