RepeatExplorer protocols

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 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 parameters5859. repeats (contigs) were then identified and classified as individual repeat clusters based on their sequence […]

2017
PMCID: 5278356
PMID: 28134354
DOI: 10.1038/srep41659

[…] 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 […]

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

[…] files and sorted using samtools [59]. 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 [60]. repeatexplorer [38] 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: 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 (novak et al., 2013) (http://repeatexplorer.org/) was used to cluster next-generation sequencing reads into groups of similar reads and to assemble contigs from these reads. […]

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

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