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DNApod workflow

The DNApod workflow process detects DNA polymorphisms and annotates them with known gene annotations. The DNApod workflow process was implemented in "DDBJ Read Annotation Pipeline (DDBJ pipeline)" (http://p.ddbj.nig.ac.jp/).
The Analytical process is shown in Fig. 1.

Fig 1. Overview of DNApod workflow.


First, the NGS reads (Fastq file) are analysed using the Basic analysis in the DDBJ Read Annotation Pipeline (DDBJ pipeline). In the Basic analysis, low quality bases of reads are trimmed, and trimmed reads are mapped to reference genome sequences. Second, the High-level analysis is started. The High-level analysis is implemented in the Virtual Machine image, which is configured the galaxy platform  Users can attempt the High-level analysis by working DNApod VM on the Pitagora-Galaxy serverThe consensus sequence file [variant call format (VCF)] is imported from the Basic analysis to the High-level analysis through the DDBJ pipeline. Homozygous SNPs/InDels are detected from the imported consensus sequence file. The DNApod workflow process visualises the distribution of homozygous SNPs/InDels in the reference genome using the DNApod original tool and annotates them with known gene structures using the snpEff tool. Details of tools and options used by the DNApod database are shown on this page. For further analysis, users can compare homozygous SNP data (VCF) detected by the DNApod workflow process with the DNApod database using the DNApod application ‘Orthologous Regions Alignment’ (Users must download the VCF file from the DNApod workflow and upload to the DNApod application ‘Orthologous Regions Alignment’).


High-level analysis (Virtual Machine Image) download



DNApod Version 0.1.0, which is based on the Pitagora-Galaxy version 0.3.1 : mac / windows
 
    ( Oracle  VirtualBox  )

DNApod workflow Manual


outline


Trial data of DNApod workflow 


[1] Beginning-start
 To attempt the DNApod workflow, we provide a trial dataset. DNApod workflow requires the user account of DDBJ pipeline. After logged in the Basic analysis of the DDBJ, you need to import SRA data (example SRA accession: DRA000010, DRA000307).  Please refer to here for the help document of SRA data import function in the DDBJ pipeline.   

[2] Middle-start
 If users want to test-use only the High-level analysis, please import  this VCF file  (reference genome: ‘Oryza sativa IRGSP build05’, snpEff database: ‘DNApod_Rice_IRGSP-RAP_build5_representative’ or ‘DNApod_Rice_IRGSP-RAP_build5_predicted’) to ‘Virtual Machine image’ for local Oracle VirtualBox or to online ‘Pitagora-Galaxy server'. For the procedure of importing the local files using Galaxy's graphical user interface, please refer to here.


Subpages (1): DNApod workflow Manual
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