NCBI submission

NCBI

BankIt

seqin: standalone application

WGS

Genome/TPA submission

• Info
• Register WGS form
• SeqIn

 /nfshomes/dpuiu/szdevel/sequin.8.10/sequin
 !!! import /nfshomes/dpuiu/bin/seqin.sqn

 Form
  Submission:
   Immediately ...
   Tentative manuscript title: 
  Contact:
   Name:  Daniela Puiu
   Phone: 301.405.3403
   Fax:   301.314.1341 
   Email: dpuiu@umiacs.umd.edu
  Authors:
   Daniela Puiu
   Steven L. Salzberg
   ...
  Affiliation
   Institution: University of Maryland,  Center for Bioinformatics and Computational Biology , Biomolecular Sciences Bldg, College Park, MD 20742 , US
  Seqeuence format
   Batch submission
   FASTA
   Original submission
  ...

 GenomeMacroSend : submit *.sqn, *.tbl, *.fsa, *agp files
 e-mail the output file to gb_sub@ncbi.nlm.nih.gov (deprecated)

TA submission

TA

Compressed archive containing 
  3 files: TRACEINFO.xml, MD5, README
  traces/ directory
  SCF format traces under traces/ or traces/*/
 
The archive(s) is/are gzip files 1-4GB; include center's name and the date into file names
Accepted only by uploading to NCBI FTP server.
  server: ftp-trace.ncbi.nih.gov
  login: 
  passwd: 
  center: UMD

Scripts:

 /nfshomes/dpuiu/Archives/JCVI/bin/phred2xmlTrace.pl

SRA submission

 server: ftp-trace.ncbi.nlm.nih.gov
 login:         cbcb_trc
 password:      t@@GeaYF
 
 Center_name (acronym): CBCB 
 Full name: Center for Bioinformatics and Computational Biology,
 University of Maryland

 Short reads: uploaded to short_read/ 
 Sanger reads: uploaded to uploads/

 Test submission: uploaded to test/ (~30 raeds)

 Validation table

AA submission

• AA
• AA submission info

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

Use XContig package scripts

Files:

.contig      : contigs & underlying reads (use TRACE_NAME's or SEQ_NAME's) 
.seq         : read sequences (use TRACE_NAME's or SEQ_NAME's) 
.qual        : read qualities (use TRACE_NAME's or SEQ_NAME's) 
.ti2seq_name : (TI , TRACE_NAME or SEQ_NAME)

 $ bank2contig -e       prefix.bnk > prefix.contig
 $ dumpreads   -e -r    prefix.bnk > prefix.seq
 $ dumpreads   -e -r -q prefix.bnk > prefix.qual

Example:

Xoo: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA

Steps:

 1. makeConinfo ASSEMBLY.coninfo
 $ more ASSEMBLY.coninfo
 <coninfo>
 <meta name='center'>UMD</meta>
 <meta name='db'>Xoo</meta>
 <meta name='desc'>Xanthomonas oryzae pv. oryzae strain PXO99A</meta>
 <meta name='object'>ASSEMBLY</meta>
 <meta name='species_code'>Xanthomonas oryzae pv. oryzae strain PXO99A</meta>
 <meta name='structure'>Chromosome</meta>
 <meta name='subtype'>NEW</meta>
 <meta name='taxid'>360094</meta>
 <contig id="1106158952778_stitched" conformation="CIRCULAR" subtype="NEW"/>
 <file src="Xoo.contig"/>
 <seq src="Xoo.seq"/>
 <qual src="Xoo.qual"/>
 <idmap  src="Xoo.ti2seq_name" direction="FORWARD"/>
 </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 ???

 3. validate:
 oXygen: software used by NCBI; license required
 xmllint: open source
 $ xmllint --schema ~/bin/TraceAssembly.xsd umd-*/ASSEMBLY.xml > /dev/null
 umd-20070816-125223/ASSEMBLY.xml validates

 4. edit files
 $ rm *.tar.gz
 $ md5sum umd-*/ASSEMBLY.xml
 $ edit umd-*/MANIFEST         # update ASSEMBLY.xml md5sum 
 
 $ ls -1 umd-*
 umd-20070816-125223/
  1106158952778_stitched_20070817-141849.con       # Contig consensus
  1106158952778_stitched_20070817-141849.congap    # Contig gaps
  ASSEMBLY.xml                                     # Assembly XML
  MANIFEST                                         # MD5 sums

4. create tarball
$ tar czvf umd-20070816-125223.tar.gz umd-20070816-125223/

5. upload tarball
   !!! contact trace@ncbi.nlm.nih.gov if login/password error
 
   $ ftp ftp-private.ncbi.nlm.nih.gov
   login: cbcb_trc
   passwd: t@@GeaYF

   $ cd assembly
   $ put *.tar.gz

TPA submissions

1. Use SeqIn : /nfshomes/dpuiu/szdevel/sequin.8.10/sequin; e-mail the output file to gb_sub@ncbi.nlm.nih.gov
2. Register WGS