DOCKS specifications

Information


Unique identifier OMICS_33392
Name DOCKS
Alternative name Design Of Compact K-mer Set for hash functions
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A list of parameters.
Output data A list of k-mers.
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Subtools


  • DOCKSany
  • DOCKSanyX

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Versioning


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Maintainer


  • person_outline Yaron Orenstein

Publication for Design Of Compact K-mer Set for hash functions

DOCKS citation

library_books

Designing small universal k mer hitting sets for improved analysis of high throughput sequencing

2017
PLoS Comput Biol
PMCID: 5645146
PMID: 28968408
DOI: 10.1371/journal.pcbi.1005777

[…] We presented the DOCKS algorithm, which generates a compact set of k-mers that together hit all L-long DNA sequences. Such compact sets have many applications in sequence analysis, including space efficient data struc […]

DOCKS institution(s)
Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA; Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
DOCKS funding source(s)
Supported in part by the Israel Science Foundation as part of the ISF-NSFC joint program 2015-2018; in part by a Ph.D. fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University; in part by an Israel Ministry of Immigrant Absorption fellowship; in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554; by the US National Science Foundation (CCF-1256087, CCF-1319998); by the US National Institutes of Health (R01HG007104) and an Alfred P. Sloan Research Fellowship.

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