NCBI submission

NCBI

BankIt

seqin: standalone application

WGS

AA

 Compressed archive containing 2 files: ASSEMBLY.xml , MD5 
 Accepted only by uploading to NCBI FTP server.
   server: ftp-private.ncbi.nlm.nih.gov
   login: umd_trc
   passwd: 
   center: UMD   
   description: University of Maryland
 ASSEMBLY XML Schema png 
 ASSEMBLY XML Schema xsd 

TA

Procedure

Files:

.contig, .seq, .qual, .seq_name2ti

Steps:

1. makeConinfo ASSEMBLY.coninfo
2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223
   problems:
    * submitter_reference="tigr...." : replace tigr with umd
    * conformation: always LINEAR    : replace LINEAR with CIRCULAR
    * taxid: not recognized          : replace <taxid>id</taxid> with <organism descriptor="TAXID">id</organism>

3. validate:
 oXygen: software used by NCBI; license required
 xmllint: open source
 $ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null