This project has been replaced with https://github.com/ddbj/mssassist

DDBJ Curators' Assistant

The system consists of:

• A set of tools designed to automate and standardize, in a fast and easy way, the curation of Sequence Datasets submitted to DDBJ. It comprises four steps: validation (ddbj_mss_validation); auto-correction (ddbj_autofix); auto upload files to DDBJ Databases (ddbj_sakura2DB); and update work tracking spreadsheet (ddbj_kaeru, "kaeru 帰る" means "leave, go home" in Japanese language, in the sense that the work is done).
• A database, named dblink_ddbj, that contains the most relevant information from DDBJ Database, designed specially for DDBJ curators.
• An easy-to-use search engine tool, search_dblink, for quickly and simultaneously retrieving data from a wide range of accession IDs.

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Mass Dataset Documentation

Notice! The MSS tool repository have been migrated to ddbj/mssassist. Please switch to /home/w3const/mssassist tools. In w3const/mssassist, update frequency of the data tables has been increased than that of the tables in /home/andrea/script.

1. DDBJ Mass Validation
   • An easy command line that identifies submitted files (annotation and fasta) and checks inconsistencies based on DDBJ rules.
   • Requirement: BioSample
   • Command line

     /home/w3const/mssassist/ddbj_mss_validation
     

   • Former command line

     bash /home/andrea/scripts/ddbj_mss_validation
     

     • Beta version

       bash /home/andrea/scripts/ddbj_mss_validation_beta
       

2. DDBJ Autofix
   • A simple command line that interactively suggests corrections that have been detected by DDBJ Mss Validation and automatically fixes them.
   • Command line

     /home/w3const/mssassist/ddbj_autofix
     

   • Former command line

     bash /home/andrea/scripts/ddbj_autofix
     

     • Beta (CAUTION! Use this version when running ddbj_mss_validation_beta)

       bash /home/andrea/scripts/ddbj_autofix_beta
       

3. DDBJ Sakura2DB
   • Interactive command line that automatically: a) identifies the file type; b) runs sakura2db (test and actual) for the corrected files to upload the files to their respective databases at DDBJ (Tsunami); c) moves the files to DONE directory.
   • Command line

     /home/w3const/mssassist/ddbj_sakura2DB
     

   • Former command line

     bash /home/andrea/scripts/ddbj_sakura2DB
     

     • Beta version

     bash /home/andrea/scripts/ddbj_sakura2DB_beta
     

4. DDBJ Kaeru
   • Update work tracking spreadsheet, after running DDBJ Sakura2DB.
   • Command line

     /home/w3const/mssassist/ddbj_kaeru
     

   • Former command line

     bash /home/andrea/scripts/ddbj_kaeru
     

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DBLink DDBJ and Search DBLink Documentation

1. DBLink DDBJ
   • Comprises essential data (dblink dataset) from the major DDBJ databases: BioProject, BioSample, Sequence Read Archive (DRA), Assembled Sequences (Mass Data) and GEA.
2. Search DBLINK
   • A simple command line tool that accesses the DBLink-DDBJ database and correlates the major DBLink dataset from DDBJ using one file with different accession IDs.