- by Mike Marquet
- this tool is under active development,feel free to report issues and add suggestions
easy way to analyze DNA Modifications of Nanopore Sequencing data
single sample analysis
multi sample analysis (every sample can use a different reference sequence)
- poreCov needs Nextflow and java run time (default-jre)
- install java run time via:
sudo apt install -y default-jre - install Nextflow via:
curl -s https://get.nextflow.io | bash && sudo mv nextflow /bin && sudo chmod 770 /bin/nextflow
- install java run time via:
- installation here (recommended), alternatively via:
sudo apt install -y docker - add Docker to the user:
sudo usermod -a -G docker $USER
### Single Sample Input
nextflow run main.nf --fasta_ref test_data/ref-fasta/barcode20.fasta --bam test_data/bam-files/barcode20.bam --output test -work-dir /home/x/Workflows/pop_the_mod/work/ -profile local,docker
### Multi Sample Input (multi reference)
nextflow run main.nf --samples test_data/multi.csv --output test/samples -work-dir /home/x/Workflows/pop_the_mod/work/ -profile local,docker
### provide a samples.csv file like this:
A,/home/x/Workflows/pop_the_mod/test_data/bam-files/barcode20.bam,/home/x/Workflows/pop_the_mod/test_data/ref-fasta/barcode20.fasta
B,/home/x/Workflows/pop_the_mod/test_data/bam-files/barcode21.bam,/home/x/Workflows/pop_the_mod/test_data/ref-fasta/barcode21.fasta
C,/home/x/Workflows/pop_the_mod/test_data/bam-files/barcode22.bam,/home/x/Workflows/pop_the_mod/test_data/ref-fasta/barcode22.fasta