Hybrid SHREC specifications

Information


Unique identifier OMICS_04060
Name Hybrid SHREC
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Source code URL https://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/BaseSpaceSHREC.zip
Maintained Yes

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Maintainer


  • person_outline Leena Salmela <>

Publication for Hybrid SHREC

Hybrid SHREC in publications

 (2)
PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] these methods can be categorized into four main classes [, ]: k-mer spectrum-based (or k-spectrum-based) (e.g., quake [], reptile [] and hammer []), suffix t-ree/array-based (hitec [], shrec [] and hybrid-shrec []), multiple sequence alignment (msa)-based (echo [] and coral []) and hidden markov model (hmm)-based (premier [] and seecer [])., since yang et al. [] last reviewed error correction […]

PMCID: 3961413
PMID: 24651535
DOI: 10.1371/journal.pone.0092663

[…] sanger and low coverage 454 data. the illumina dataset was error-corrected using reptile . the 454 datasets were pooled with the reptile corrected illumina reads and errors were then corrected using hybrid-shrec . the clustering tool cd-hit-est was used to generate a non-redundant dataset that contains only unique contigs from all abyss assemblies. the final merged illumina dataset (abyss_sol) […]


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Hybrid SHREC institution(s)
Department of Computer Science, University of Helsinki, Finland
Hybrid SHREC funding source(s)
Supported by the Academy of Finland [grant number 118653 (ALGODAN)].

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