A collection of scripts to get started with running the REPET pipeline on a cluster with the SLURM resource manager and a module system installed.

1. FASTA Format
   • Header
     • Recommended format: ">XX_i" (XX = letters, i = numbers)
     • avoid spaces and symbols like "=;:|"
   • 60 bps (or less) per line for sequences

1. Host genome (FASTA format)
2. REPET-specific Pfam HMM File
3. rDNA (FASTA format) of host genome
   • RNAmmer
4. RepBase Amino Acid Database
5. RepBase Nucleotide Database
6. cDNA of host genome (FASTA format)

A RepeatScout bank can also be provided but there are additional pre-processing steps before it can be used in the pipeline. See the TEdenovo tuto webpage or text file included with REPET. These scripts currently do NOT perform this pre-processing steps.

1. Host genome (FASTA format)
2. TE library (FASTA format)
   • from TEdenovo or another source
3. RepBase Amino Acid Database
4. RepBase Nucleotide Database

1. Clone the repository and copy the default configuration.

$ git clone https://github.com/stajichlab/REPET-slurm
$ cd REPET-slurm/TEdenovo
$ cp /path/to/REPET/config/TEdenovo.cfg .

2. Change the settings in TEdenovo.cfg and TEdenovo_AllSteps.sh to match your environment/project.
3. Copy/link the prerequisite files into the TEdenovo folder.
4. sh TEdenovo_AllSteps.sh or sbatch TEdenovo_AllSteps.sh.

If you already ran TEdenovo, then skip step 1.

1. Clone the repository and copy the default configuration.

$ git clone https://github.com/stajichlab/REPET-slurm
$ cd REPET-slurm/TEannot
$ cp /path/to/REPET/config/TEannot.cfg .

2. Change the settings in TEannot.cfg and TEannot_AllSteps.sh to match your environment/project.
3. Copy/link the prerequisite files into the TEannot folder.
   • TE library has a required naming format: <project_name>_refTEs.fa
4. sh TEannot_AllSteps.sh or sbatch TEannot_AllSteps.sh.