RepeatExplorer pipeline

RepeatExplorer specifications

Information


Unique identifier OMICS_07465
Name RepeatExplorer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.9.7.8
Stability Stable
Maintained Yes

Publications for RepeatExplorer

RepeatExplorer citations

 (5)
2017
PMCID: 5704207

[…] b chromosome-enriched sequences, such as satellite dna, retrotransposons, and organelle-derived sequences, can be identified by the similarity-based clustering of ngs reads, as attempted by the repeatexplorer pipeline, which identifies clusters of frequently overlapping reads, and interprets these as parts of repetitive elements [61]. in addition, the pipeline estimates copy numbers, based […]

2017
PMCID: 5893959

[…] annotated as similar to phi-x174 were removed as contaminants. the output of repeatexplorer was also used to prepare an in-house library containing all contigs belonging to clusters annotated by repeatexplorer as ltr-res by similarity search against repbase [40]. subsequently, pairwise hybrid clustering between a random set of 1,431,114 illumina reads derived from p. micrantha genomic dna […]

2017
PMCID: 5278356

[…] first, the input dna was sequenced using hiseq 2500 platform. a portion of randomly selected input-seq reads were used to perform graph-based clustering using the repeatexplorer software (http://repeatexplorer.umbr.cas.cz/) with default parameters5859. repeats (contigs) were then identified and classified as individual repeat clusters based on their sequence similarity. second, the chip-seq […]

2016
PMCID: 4943200

[…] was prefixed to each sequence name, after which we combined genomic samples from all 13 accessions into a single data set for analysis (table 1)., the combined sequence reads were analyzed using the repeatexplorer pipeline (novak et al. 2010, 2013), which identifies repetitive dna families in low-pass, next-generation sequence data and has been used successfully in other species (macas et al. […]

2015
PMCID: 4659654

[…] data for p. sativum was generated earlier using the same technology [37]., repeat identification by similarity-based clustering of illumina reads was performed using local installation of the repeatexplorer pipeline [32] which was run on a debian linux server with 32 cpu cores and 64 gb ram. the pipeline employs graph representation of read similarities to identify clusters of frequently […]

RepeatExplorer institution(s)
Institute of Plant Molecular Biology, Biology Centre ASCR, České Budějovice, CZ, Czech Republic

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