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Jellyfish | A lock-free approach for parallel counting of occurrences of k-mers

A k-mer counting algorithm. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution.

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Jellyfish classification

Jellyfish specifications

Unique identifier:
OMICS_01056
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

Jellyfish distribution

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Publications

Institution(s)

Program in Applied Mathematics, Statistics and Scientific Computation, University of Maryland, College Park, MD, USA; Department of Computer Science and Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA

Funding source(s)

National Science Foundation (grants EF-0849899 and IIS-0812111); National Institutes of Health (grant 1R21AI085376); National Science Foundation (grant DMS-0616585); National Institutes of Health (grant 1R01HG0294501)

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.