BFCounter is a program for counting k-mers from DNA sequencing data it uses a Bloom filter data structure to filter unique k-mers, likely generated from sequencing errors. Counting k-mers (substrings of length k) is an essential compononet of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting k-mers in large modern sequence data sets can easily overwhelm the memory capacity of standard computers. In current data sets, a large fraction – often more than 50% – of the storage capacity may be spent on storing k-mers that contain sequencing errors and which are typically observed only a single time in the data. These singleton k-mers are uninformative for many algorithms without some kind of error correction.
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Melsted, P. and Pritchard, J.K.:
Efficient counting of k-mers in DNA sequences using a bloom filter
BMC Bioinformatics 2011 12:333.