git clone https://github.com/WSG-Lab/ECCFP.git
cd ECCFP
pip install .

eccfp --fastq input.fastq --paf mapping.paf --reference ref.fa -o output

usage: eccfp.py [options]

options:
  -h, --help            show this help message and exit

  Generate candidate eccDNA from rolling circle reads:

  --fastq FASTQ         input reads in fastq format
  --paf PAF             input alignments in PAF format
  --reference REFERENCE
                        reference genome sequences in fasta format
  --output OUTPUT, -o OUTPUT
                        output folder, the default is the current folder
  --maxOffset MAXOFFSET
                        maximum offset of start/end positions between two sub-reads to be considered as mapping to the same location, default is 20
  --minMapQual MINMAPQUAL
                        minimum mapping quality of sub-reads, default is 30

  Get accurate eccDNA location from candidate eccDNA:

  --fluctuate FLUCTUATE
                        maximum offset between the candidate eccDNA and the candidate eccDNA in a group, default is 20bp
  --nf NF               minimum number of fullpass to support candidate eccDNA, default is 2
  --cov COV             minimum fullpass used for merging a set of candidate eccDNA, default is 1
  --nc NC               minimum number of candidate eccDNA required to merge overlapped candidate eccDNAs, default is 2

  Generate consensus sequences and variants:

  --minDP MINDP         minimum depth to call variants, default is 4
  --minAF MINAF         minimum alternative allele frequency to call variants, default is 0.75

cd example
minimap2 -cx map-ont ref.fa example.fastq --secondary=no -t 8 -o mapping.paf
eccfp --fastq example.fastq --paf mapping.paf --reference ref.fa -o output