RepeatMasker protocols

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RepeatMasker statistics

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RepeatMasker specifications


Unique identifier OMICS_09436
Name RepeatMasker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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Unique identifier OMICS_09436
Name RepeatMasker
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

RepeatMasker in pipelines

PMCID: 5755439
PMID: 29304732
DOI: 10.1186/s12864-017-4421-z

[…] genes were confirmed by using blast+ (version 2.2.31) against the ncbi non-redundant database (nr) with an e-value cutoff of 1e−5. dispersed repeated sequences were predicted with the software of repeatmasker through aligning the genome sequence with repeat databases (eg. repbase); tandem repeats (tr) were searched via trf (tandem repeats finder). trs were first modelled by percentage […]

PMCID: 5758801
PMID: 29311560
DOI: 10.1038/s41598-017-18308-8

[…] against the human reference genome (grch37.p13) downloaded from the reference sequence (refseq) collection. in this alignment process, we also considered repetitive elements defined by the output of repeatmasker that was downloadable from refseq. based on these alignments, we calculated the read counts for each genomic position by using in- house software that uniformly divided each multi-mapped […]

PMCID: 5775534
PMID: 29351814
DOI: 10.1186/s13059-017-1376-y

[…] mm9 using tophat v2.0.9 [] with -g 1 option, which assigns reads with multiple hits of equal quality to one of those locations at random (i.e., “inclusive mapping”). raw read counts for each gene or repeatmasker class were used in deseq2 for differential expression analysis and for generating normalised gene and repeat expression values. for expression analysis of individual iap copies, […]

PMCID: 5785820
PMID: 29416570
DOI: 10.1186/s13148-018-0446-7

[…] mapping reads were kept []. unmapped reads were aligned first ribosomal sequences allowing for up to 10 mappings per read, reads that were still unmapped were aligned to mirna-, pirna-, trna- and repeatmasker-sequences in that order, keeping only reads that could be uniquely mapped. reads that mapped to the genome in the first step were counted using feature counts [], assigning reads […]

PMCID: 5797644
PMID: 29441061
DOI: 10.3389/fimmu.2018.00030

[…] alignment to the reference genome, and filtering were done using bwa, samtools, picard, bedtools, and phantompeakqualtools software. the aligned tfbs were mapped on the re sequences annotated by repeatmasker and downloaded from the uscs browser (repeatmasker table). tfbs occurrence data were extracted from the bedgraph files. the fold change over control profiles for tfbs, as well […]

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RepeatMasker in publications

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] genomes were assembled with ray v2.3.1 (). the scaffolds of s. simulii were built using sspace (). satellites, simple repeats, and low-complexity sequences were annotated with repeatmasker v4.0.5 ( and tandem repeat finder v4.07b (), corresponding to fungal sequences from repbase (). the genomes were annotated with the funannotate v0.6.2 […]

PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

[…] tags matching protein-coding sequences were eliminated from the data set. to remove tags corresponding to low-complexity sequences including rrna, trna, snrna, and snorna, reads were screened using repeatmasker ( and compared with entries in the rfam database ( the remaining sequences were considered as candidate mirnas. with mirbase […]

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] gapcloser v1.12 [, ]. the completeness of the c. pseudoreteaudii genome was evaluated using cegma []. repeat sequences were identified and classified using repeatmodeler v1.07, repeatproteinmask and repeatmasker v4-0-3., gene structure was predicted using the pasa pipeline with a combination of ab-initio and rna-seq evidence based approaches []. for ab-initio predictions, augustus, snap, […]

PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] altered chromatin accessibility were mapped to genomic annotations or repeat regions using bedtools v2.26.0. for the genomic annotations, we used tsss from the fantom database, repeats from repeatmasker (ucsc genome browser) and other genomic features (exons, introns, utrs, etc.) were extracted from the ucsc table browser. the enhancers were identified based on our own h3k4me1 […]

PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] feasibility, the three assemblies used kmer values of 63, 63, and 35 respectively, and we merged scaffolds with metassembler v1.5 []. we estimated proportions of repetitive elements with repeatmasker v4.0.5 using the “aves” repeat library []., we annotated scaffolds with a length of 1 kb or greater using maker v2.31.8 [] and conducted gene predictions using augustus v3.2.1 [] […]

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