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BFCounter | Counting of k-mers in DNA sequences using a bloom filter

Identifies all the k-mers that occur more than once in a DNA sequence data set. BFCounter does this using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements. We then make a second sweep through the data to provide exact counts of all nonunique k-mers. For example data sets, we report up to 50% savings in memory usage compared to current software, with modest costs in computational speed. This approach may reduce memory requirements for any algorithm that starts by counting k-mers in sequence data with errors.

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BFCounter classification

BFCounter specifications

Unique identifier:
OMICS_02093
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Computer skills:
Advanced
Maintained:
Yes

BFCounter distribution

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BFCounter support

Maintainer

  • Jonathan K. Pritchard <>

Credits

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Publications

Institution(s)

Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA

Funding source(s)

A grant from the National Institutes of Health: MH084703; the Howard Hughes Medical Institute

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