Nextflow Modules
Showing module(s) with keyword "repeat"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/fasta_explore_search_plot_tidk | Workflow | genomics telomere repeat search plot | Uses Telomere Identification toolKit (TIDK) to identify the frequency of telomeric repeats along a sliding window for each sequence in the input fasta file. Results are presented in TSV and SVG formats. The user can specify an a priori sequence for identification. Possible a posteriori sequences are also explored and the most frequent sequence is used for identification similar to the a priori sequence. seqkit/seq and seqkit/sort modules are also included to filter out small sequences and sort sequences by length. |
| nf-core/gt/ltrharvest | Process | genomics genome annotation repeat transposons retrotransposons | Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility |
| nf-core/ltrfinder | Process | genomics annotation parallel repeat long terminal retrotransposon retrotransposon | Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder |
| nf-core/ltrharvest | Process | genomics genome annotation repeat transposons retrotransposons | Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest utility included in the EDTA toolchain |
| nf-core/ltrretriever/lai | Process | genomics annotation repeat long terminal retrotransposon retrotransposon stats qc | Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments |
| nf-core/ltrretriever/ltrretriever | Process | genomics annotation repeat long terminal repeat retrotransposon | Identifies LTR retrotransposons using LTR_retriever |
| nf-core/panteraga | Process | genome alignment transposable elements repeat annotation | Identification of transposable element families from whole genome alignments using FastGA |
| nf-core/repeatmasker/repeatmasker | Process | genome annotation repeat mask | Screening DNA sequences for interspersed repeats and low complexity DNA sequences |
| nf-core/repeatmodeler/builddatabase | Process | genomics fasta repeat | Create a database for RepeatModeler |
| nf-core/repeatmodeler/repeatmodeler | Process | genomics fasta repeat transposable element | Performs de novo transposable element (TE) family identification with RepeatModeler |