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FACS | Classification of DNA sequences using Bloom filters

Allows to assembly filters from genome sequences and apply a filter to a file of sequence reads. FACS classifies sequence reads as belonging to one of many reference sequences or being ‘novel’. The software transforms the reference sequence into Bloom filters, and then the Bloom filters can be queried for exact matches. This method allows rapid classification of sequences using references as large as the human genome.

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FACS classification

FACS specifications

Unique identifier:
Software type:
Restrictions to use:
Operating system:
GNU General Public License version 2.0, MIT License
Fast and Accurate Classification of Sequences
Command line interface
Output format:
Programming languages:
C, Perl, Python
Computer skills:

FACS distribution


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FACS support



  • Henrik Stranneheim <>
  • Joakim Lundeberg <>

Additional information


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Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden; LingVitae AB, Stockholm, Sweden; Department of Microbiology, Laboratory for Clinical Microbiology, Tumorand Cell Biology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; School of Computer Science and Communication, Stockholm Bioinformatics Center, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden

Funding source(s)

Supported by the Swedish Research Council (grant number 2006-6022).

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