RepeatScout protocols

RepeatScout specifications

Information


Unique identifier OMICS_03540
Name RepeatScout
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0.5
Stability Stable
Maintained Yes

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Documentation


Publication for RepeatScout

RepeatScout IN pipelines

 (3)
2016
PMCID: 4736629
PMID: 26833063
DOI: 10.1186/s12870-016-0725-4

[…] an abundant tandem repeat that accounts for more than 4 % of the whole teff genome., half a million paired-end reads representing 0.25× coverage of the e. tef genome were analyzed using repeatscout [39], a program that has proven effective in de novo identification of repeats. reads were assembled into consensus sequences using cap3 [40], and consensus sequences were clustered […]

2016
PMCID: 4752745
PMID: 26873713
DOI: 10.1186/s13073-016-0274-3

[…] filtered to remove sites with a quality score less than 50, less than four reads covering the snp site, and a snp/mapping quality ratio less than 0.75. snps in repeat regions identified using repeatscout [30] and mobile genetic elements were excluded. this resulted in 24,660 snps from the core genome. sequence data were deposited in the european nucleotide archive (project accession […]

2008
PMCID: 2657916
PMID: 19077187
DOI: 10.1186/1471-2164-9-595

[…] of 60 identical nucleotides every 100 bp., to identify all the repetitive elements present in the e. histolytica genome, 1499 scaffolds from the current genomic sequence data were surveyed using repeatscout or an all-versus-all comparison approach as described in methods. in a preliminary screening, all known elements and new repetitive sequences above 400 bp were selected […]

RepeatScout institution(s)
Department of Computer Science and Engineering, University of California San Diego La Jolla, CA, USA

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