akiomiyao/ped repository overview

⁠Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

The PED is a unique detection system of DNA polymorphism (mutation) from sequence data generated by next-generation sequencer.

⁠Usage

docker run -w /ped -v /home/your_account/your_working_directory:/work akiomiyao/ped perl download.pl accession=accession,wd=/work  
docker run --init -w /ped -v /home/your_account/your_working_directory:/work akiomiyao/ped perl ped.pl target=target,control=control,ref=reference,wd=/work  

Free of use for academics.
Please read README.md in the ped directory or access to https://github.com/akiomiyao/ped⁠
Citation : Miyao, A., Kiyomiya, J.S., Iida, K. et al. Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.
BMC Bioinformatics 20, 362 (2019). https://doi.org/10.1186/s12859-019-2955-6⁠

⁠Demonstration

Update docker container.

mkdir ped
cd ped
mkdir work
docker pull akiomiyao/ped

Detection of mutations in SARS-CoV-2.
Download fastq files of SRR11513115.

docker run -w /ped -v `pwd`:/work akiomiyao/ped perl download.pl accession=SRR11513115,wd=/work

Detection

docker run --init -w /ped -v `pwd`:/work akiomiyao/ped perl ped.pl target=SRR11513115,ref=SARS-CoV-2,wd=/work

Detection of SNPs and structural variations between nematodes.
Download fastq files of ERR3063486 and ERR3063487 in NCBI/SRA. Downloading requires several hours.

docker run -w /ped -v `pwd`:/work akiomiyao/ped perl download.pl accession=ERR3063486,wd=/work  
docker run -w /ped -v `pwd`:/work akiomiyao/ped perl download.pl accession=ERR3063487,wd=/work  

Detection of SNPs and structural variations between ERR3063486 and ERR3063487.

docker run --init -w /ped -v `pwd`:/work akiomiyao/ped perl ped.pl target=ERR3063487,control=ERR3063486,ref=WBcel235,wd=/work  

ERR3063487 sequences of Caenorhabditis elegans nematode are 250 generations after ERR3063486.

Results will be saved in the ERR3063487 directory.