SCALCE protocols

SCALCE specifications


Unique identifier OMICS_00969
Alternative name Sequence Compression Algorithm using Locally Consistent Encoding
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Sequence Compression Algorithm using Locally Consistent Encoding

SCALCE IN pipeline

PMCID: 5645146
PMID: 28968408
DOI: 10.1371/journal.pcbi.1005777

[…] k-mer occurrences. the locally consistent parsing (lcp) [13] algorithm provides the concept of “core substrings” which, like minimizers, are guaranteed to be shared by long enough identical strings. scalce [14] uses core substrings to compress dna sequences., a small uhs, if it can be found, has a number of advantages over minimizers for these applications:, the set of minimizers for a given […]

SCALCE institution(s)
School of Computing Science, Simon Fraser University, Burnaby, Canada
SCALCE funding source(s)
Natural Sciences and Engineering Research Council of Canada (NSERC); Bioinformatics for Combating Infectious Diseases Project (BCID); Michael Smith Foundation for Health Research grants; Canadian Research Chairs Program; an NIH grant HG006004

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