rwt is a set of small utilies for making reference genomes/transcriptomes that contain additional records, such as consensus transposable element sequence.
Currently, most utilites are written with consensus TE sequences from RepBase in mind.
Runs Repeatmasker.
Outputs your.fa.{tbl, out, masked, cat} to the directory of your choosing ('./' by default).
Files fitting this pattern will be removed prior to running rwt.
rwt mask your.fa repbase.fa
Removes '#' from record names in RepBase lib.
rwt clean_repbase_fa repbase.fa repbase.clean.fa
Makes a gtf with a record for each sequence in a fasta.
rwt fa2gtf repbase.clean.fa repbase.gtf
# from source
cd reference-with-transposons
pip install .
# from conda
conda install -c mal2017 rwt
# singularity/docker
... in progress ...
- R
- multiple tidyverse packages
- rtracklayer
- RepeatMasker