RepeatModeler

RepeatModeler is a de novo transposable element family identification and modeling package. RepeatModeler consists of 3 core programs (RECON, RepeatScout, and LtrHarvest/Ltr_retriever) that identify repeat element boundaries and family relationships from sequencing data.

For input, it takes a database and an input sequence. It outputs 3 primary files: families.fa, families.stk, and rmod.log. families.fa consists of the consensus sequences, .stk consists of seed alignments, and rmod consists of a summarized log of the run. Note that this program generates a large volume of temporary files that are not automatically cleaned up between runs. You will have to manually clean your directory between runs. Also note that RepeatModeler generally requires long runtimes, so you must plan your resource request accordingly. This module also loads BuildDatabase and RepeatClassifier.

For additional information and examples, see the RepeatModeler documentation.

ml biocontainers repeatmodeler
BuildDatabase -name fish fish.fa
RepeatModeler -database fish -threads # -LTRStruct

Parallel Capabilities: Single core default, multithreading options supported.