RepARK pipeline

RepARK specifications

Information


Unique identifier OMICS_03446
Name RepARK
Alternative name Repetitive motif detection by Assembly of Repetitive K-mers
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Input data can be one or more fasta or fastq files.
Output data The repeat consensuses can be found in the file repeat_lib.fasta within the working directory.
Operating system Unix/Linux
Computer skills Advanced
Version 1.3.0
Stability Stable
Requirements Jellyfish, Velvet, CLC Assembler
Maintained Yes

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Documentation


Maintainer


  • person_outline Philipp Koch <>

Publication for Repetitive motif detection by Assembly of Repetitive K-mers

RepARK IN pipelines

 (2)
2015
PMCID: 4433549
PMID: 25573702
DOI: 10.1093/aobpla/plu086

[…] citrus sinensis, using bowtie2 (langmead and salzberg 2012, settings -d 20 -r 3 -n 1 -l 20 -i s,1,0.50 -a)., reads from the highly repeated fraction of the genome were extracted and assembled using repark (repetitive motif detection by assembly of repetitive k-mers; koch et al. 2014). the motifs present in the repetitive contigs were counted and analysed by blastn (e-value 1e-5) against repbase […]

2015
PMCID: 4433549
PMID: 25573702
DOI: 10.1093/aobpla/plu086

[…] sinensis, using bowtie2 (langmead and salzberg 2012, settings -d 20 -r 3 -n 1 -l 20 -i s,1,0.50 -a)., reads from the highly repeated fraction of the genome were extracted and assembled using repark (repetitive motif detection by assembly of repetitive k-mers; koch et al. 2014). the motifs present in the repetitive contigs were counted and analysed by blastn (e-value 1e-5) against repbase v19.08 […]

RepARK institution(s)
Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
RepARK funding source(s)
Klaus Tschira Stiftung [00.179.2011]

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