RepeatExplorer protocols

View RepeatExplorer computational protocol

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RepeatExplorer specifications

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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 in pipelines

 (16)
2017
PMCID: 5278356
PMID: 28134354
DOI: 10.1038/srep41659

[…] centromeric repetitive sequences. 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 parameters. repeats (contigs) were then identified and classified as individual repeat clusters based on their sequence […]

2017
PMCID: 5480163
PMID: 28637491
DOI: 10.1186/s13059-017-1249-4

[…] bam files and sorted using samtools []. read coverage and enrichment were displayed after converting bam files to tdf files with means of 20,000 kb intervals using the integrative genome viewer []. repeatexplorer [] was used to cluster reads independently of genome alignment from each input sample (default parameters). circular consensus sequences from each set of reads in the centc cluster […]

2017
PMCID: 5555486
PMID: 28659292
DOI: 10.1534/g3.117.042093

[…] (erx2037878) sequence reads (20× coverage) were generated by our group (dias et al., unpublished data)., similarity-based clustering, repeat identification, and classification were performed using repeatexplorer () with whole-genome shotgun illumina reads from d. buzzatii, d. mojavensis, and d. seriema. initially, files containing all sequence reads from each species were uploaded (trimmed […]

2017
PMCID: 5563062
PMID: 28821238
DOI: 10.1186/s12864-017-4050-6

[…] analysis of the distribution of divergence values between pairwise comparisons of sequences belonging to the same lineage., after collecting chromovirus rt domain-related sequences (90 nt-long) from repeatexplorer, cluster mapping was performed using clc-bio genomic workbench for isolating reads homologous to rt in each species or subspecies. then, paralogous reads were pairwise compared (using […]

2017
PMCID: 5669256
PMID: 29104828
DOI: 10.7717/peerj.3982

[…] hiseq 2500 platform on a single lane. clean sequencing data were supplied in fastq format without adapters. the raw data has been deposited in ncbi sra database (accession number: srr6038670)., the repeatexplorer pipeline () (http://repeatexplorer.org/) was used to cluster next-generation sequencing reads into groups of similar reads and to assemble contigs from these reads. as shown in , […]


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RepeatExplorer in publications

 (58)
PMCID: 5895790
PMID: 29643436
DOI: 10.1038/s41598-018-24196-3

[…] putative satellite repeats were identified based on the properties of cluster graphs obtained by similarity-based clustering of low-pass genome sequencing illumina reads, as implemented in the repeatexplorer pipeline. these graphs represent the reads and their sequence similarities as nodes and connecting edges, respectively, and form globular or ring-like shapes in the case of tandem […]

PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] can also be discerned through genome skim data. although multiple studies have focused on the use of longer read technology such as 454 pyrosequencing (e.g., harkess et al., ), the development of repeatexplorer (novák et al., ) and transposome (staton and burke, ) enable short reads to be used for transposon identification (e.g., staton and burke, ). using these approaches, genome skim data […]

PMCID: 5895188
PMID: 29732260
DOI: 10.1002/aps3.1030

[…] elements in a genome can also be inferred by shotgun illumina dna sequencing data before assembly. sequence reads that cover as little as 1% of the genome size can be used as input to programs like repeatexplorer (available as a free galaxy server at http://www.repeatexplorer.org/; novák et al., ) or transposome (staton and burke, ). random, low‐coverage shotgun reads are clustered […]

PMCID: 5819184
PMID: 29458354
DOI: 10.1186/s12864-018-4547-7

[…] tool []. all 14 datasets were randomly sampled to represent approximately 0.015×/1c (the exact number of reads is shown in additional file : table s4) and 3,479,090 reads were analyzed altogether. repeatexplorer pipeline [, ] was used for de novo repeat identification. resulting clusters were characterized based on similarity searches against repeatmasker libraries, user custom libraries, […]

PMCID: 5767042
PMID: 29329524
DOI: 10.1186/s12862-017-1113-x

[…] paired-end reads were joined using the “fastq-join” software of the fastx-toolkit suit [] with default options. to search for satdnas in the r. bergii genome, 4,702,802 joined reads were used in the repeatexplorer pipeline [, ]. we then searched for clusters showing higher graph density, which is a typical feature of satdnas families analysis [, ] due to tandem repeats characteristic […]


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

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