The next step is to mask and annotate repeats with RepeatModeler and RepeatMasker.

RepeatModeler is a repeat-identifying software that can provide a list of repeat family sequences to mask repeats in a genome with RepeatMasker. For more information, or to download, visit RepeatModeler.

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. the output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked. For more information, or to download, visit RepeatMasker.

We will apply this software in the following steps:

1) Build a database for RepeatModeler

2) Run RepeatModeler

3) Run RepeatMasker to annotate repeats

1 Build a Database for RepeatModeler

This can be run on an interactive node, or by submitting a job with the following code:

#build database
BuildDatabase -name database_name /path/to_assembly/file.fasta
#
#Explanation
#-name: name to be given to the database
#genome file in fasta format

2 Run RepeatModeler

Write and submit a job script with the following code:

echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS
#
RepeatModeler -database databasa_name -pa 36 -engine ncbi > repeatmodeler_cl_out.log
#
echo = `date` job $JOB_NAME done
#
#Explanation
#-database: The prefix name of a XDF formatted sequence database containing the genomic sequence to use when building repeat models
#-pa: number of cpus
#-engine: The name of the search engine we are using. I.e abblast/wublast or ncbi (rmblast version).
#Note the new version of repeatmodeler calls another program called LTRStruct.
#-LTRStruct: enables the optional LTR structural finder.

3 Run RepeatMasker to Annotate Repeats

Write and submit a job script with the following code:

echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS
#
RepeatMasker -pa $NSLOTS -xsmall -gff -lib consensi.fa.classified -dir ../repeatmasker /path/to_assembly/file.fasta
#
echo = `date` job $JOB_NAME done
#
#Explanation
#-lib: repeatmodeler repbase database to be search
#-pa: number of cpus
#-xsmall: softmasking (instead of hardmasking with N)
#-dir ../repmasker: writes the output to the directory repmasker
#-gff: output format of the annotated repeats