RepeatModeler protocols

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description
RepeatModeler computational protocol

RepeatModeler specifications

Information


Unique identifier OMICS_19729
Name RepeatModeler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Open Software License v. 2.1
Computer skills Advanced
Version 1.0.10
Stability Stable
Requirements
RepeatMasker & Libraries, RECON, RepeatScout, TRF, NSEG, RMBlast, ABBlast/WUBlast
Maintained Yes

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RepeatModeler IN pipelines

 (4)
2018
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] in the a. limnaeus genome is much higher than other teleost species such as gasterosteus aculeatus (stickleback) and gadus morhua (cod), but is very similar to n. furzeri and d. rerio (table 1). repeatmodeler was able to detect approximately 30% of the assembled genome as repetitive elements (table 7).table 7 a. limnaeus d. rerio repeat masker %27.55–tandem repeat finder %3.13–total % […]

2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] and combined with 548 repetitive sequences from the repbase database [42]. the repbase sequences originated from the salmoniformes family, and excluded simple repeats (downloaded january 13, 2017). repeatmodeler v1.0.8 [43] was also used together with the allpaths-lg initial assembly in a de novo approach, which identified 1,124 repetitive sequences., the repetitive sequences were then aligned […]

2016
PMCID: 4775049
PMID: 26934481
DOI: 10.1371/journal.pone.0150573

[…] considering paired-end reads, with clustering and assembly overlap lengths equal to 55 and 40 bp, respectively. for this analysis, we also built a custom database of repeated sequences by running repeatmodeler [32] on the assembled a. mexicanus genome (genbank accession number apwo00000000.1) as a complement to repbase for cluster annotation. this custom database resulted in 1,243 sequences, […]

2014
PMCID: 4367827
PMID: 25527032
DOI: 10.1186/1471-2164-15-1153

[…] the median coverage rather than the mean coverage was used. variation of the mapping quality filter (e.g. q as low as 10 or 20) resulted in only small changes in the coverage estimates., repeatmodeler was run on the final b. tryoni assembly following the authors’ instructions. the 18-mer extension method began with jellyfish program [18], which was used to estimate 18-mer frequencies […]

RepeatModeler funding source(s)
Supported by the NIH (R44 HG02244 and R01 HG002939) and the Institute for Systems Biology.

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