mal2017/genome-plus-repeats

For Tidalbase TEs, non-Dmel seqs can be removed with the seqkit command below. This works for Tidalbase because Dmel TEs don't have 'Dmel' in the name, but other TEs have the 4 letter species abbreviation.

# seqkit 2.3.1
seqkit grep -r -n -v -p "\\|D.{3}\\\\" Tidalbase_transposon_sequence.fasta > repeats.fasta

The pipeline can be run with

NXF_CONDA_ENABLED=true nextflow run main.nf \
    --extra_fasta repeats.fasta \
    --genome_fasta dmel-all-chromosome-r6.41.fasta.gz \
    --genome_gtf dmel-all-r6.41.gtf.gz

After running the nextflow script, fix_seqnames.R can be run and used for ptera