Installation

Availability

circfull source code is available at:

Dependencies

Install the following tools before running circfull:

  • minimap2 (>=2.1)

  • bedtools (>=2.29.2)

  • samtools (>=1.6)

  • porechop (0.2.4)

The circfull repository also includes TideHunter (1.0) and TRF (4.09).

Python 3 is required with these packages:

  • pysam

  • numpy

  • pandas

  • python-intervals

  • pyfasta

  • sklearn

  • interval

  • mappy

  • progressbar

  • docopt

Install from pip

pip install circfull

Install from source

git clone https://github.com/yangence/circfull.git
cd circfull/script
pip install -r requirements.txt
python setup.py install

If installing pyfasta fails with pip, try installing it via conda.

Required reference files

1. Indexed genome FASTA

samtools faidx $genome

2. Tabix-indexed gene annotation GTF

grep -v '#' $gtf | sort -k 1,1 -k 4,4n | bgzip > sort.gtf.gz
tabix sort.gtf.gz

3. Repetitive elements (optional)

Optional repetitive-element annotations can be downloaded from: