CReSIL: Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences

A tool for detecting eccDNA from Nanopore reads

Installation instructions

## Install Conda environment
cd cresil
conda env create -f environment.yml

## Activate CReSIL environment
conda activate cresil

## Install CReSIL
pip install .

Testing (Human eccDNA)

## Go to an example folder
cd example

## Run trim 
cresil trim -t 4 -fq exp_reads.fastq -r reference.mmi -o cresil_result

## Run eccDNA identification for enriched data
cresil identify -t 4 -fa reference.fa -fai reference.fa.fai -fq exp_reads.fastq -trim cresil_result/trim.txt

## Run eccDNA annotation
cresil annotate -t 4 -rp reference.rmsk.bed -cg reference.cpg.bed -gb reference.gene.bed -identify cresil_result/eccDNA_final.txt

## Run visualize eccDNA (ec1)
cresil visualize -t 4 -c ec1 -identify cresil_result/eccDNA_final.txt

## Run Circos (ec1)
cd cresil_result/for_Circos/ec1
circos -noparanoid -conf circos.conf

The structure of files and directories generated from CReSIL is as follows:

cresil_result/
├── trim.txt
├── eccDNA_final.txt
├── cresil_run/
│   ├── subGraphs.summary.txt
│   ├── tmp/
│   └── assemGraph/
│       ├── ec1/
│       ├── ec2/
│       └── ..
├── cresil_gAnnotation/
│   ├── gene.annotate.txt
│   ├── CpG.annotate.txt
│   ├── repeat.annotate.txt
│   └── variant.annotate.txt
└── for_Circos/
    └── ec1/
        ├── circos.conf
        ├── ticks.conf
        ├── ideogram.conf
        ├── karyotype.conf
        ├── data/
        └── tmp/

For more details about mapped reads for each eccDNA, please see the eccDNA folder in assemGraph.

Additional useful commands

To run CReSIL to identify eccDNA in a relaxed mode (from the trimming step)

## Run eccDNA identification for with minimizing parameters (minimum size of eccDNA, average depth, number of supported breakpoints)
cresil identify -t 4 -minrsize 40 -depth 1 -break 1 -fa reference.fa -fai reference.fa.fai -fq exp_reads.fastq -trim cresil_result/trim.txt

To use CReSIL to identify eccDNA in whole-genome long-read (WGLS) sequencing data (from the trimming step)

## Run eccDNA identification for whole-genome long-read (WGLS) sequencing data
cresil identify_wgls -t 4 -r reference.mmi -fa reference.fa -fai reference.fa.fai -fq exp_reads.fastq -trim cresil_result/trim.txt

Interface

cresil trim - find and trim potential eccDNA regions from ONT reads
cresil identify - identify and verify eccDNA from enriched data
cresil identify_wgls - identify and verify eccDNA from whole-genome long-read (WGLS) sequencing data
cresil annotate - annotate identified eccDNA
cresil visualize - generate Circos configuration files for specified eccDNA

Sample data

References and simulated data for the user to go through the example of CReSIL pipeline and used in the CReSIL benchmarks.

References
Simulated data

Citation

Please cite the following article if you use CReSIL in your research

Visanu Wanchai, Piroon Jenjareonpun, Thongpun Leangapichat, Gerard Arrey, Charles M Burnham, Maria C Tümmle, Jesus Delgado-Calle, Birgitte Regenberg, Intawat Nookaew, CReSIL: Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences, Briefings in Bioinformatics. 2022;, bbac422, https://doi.org/10.1093/bib/bbac422.

License and Copyright

CReSIL is distributed under the terms of the MIT License

visanuwan / cresil

readme