NCBI submission: Difference between revisions
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[http://www.ncbi.nlm.nih.gov/Genbank/wgs.html WGS] | [http://www.ncbi.nlm.nih.gov/Genbank/wgs.html WGS] | ||
== TA submission == | |||
[http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=submit&m=doc&s=submit TA] | |||
== AA submission == | |||
[http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=rfc&m=doc&s=rfc AA] | [http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi?cmd=show&f=rfc&m=doc&s=rfc AA] | ||
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[[Media:ASSEMBLY.png|ASSEMBLY XML Schema png]] | [[Media:ASSEMBLY.png|ASSEMBLY XML Schema png]] | ||
[[Media:ASSEMBLY.xsd|ASSEMBLY XML Schema xsd]] | [[Media:ASSEMBLY.xsd|ASSEMBLY XML Schema xsd]] | ||
Use XContig package scripts | Use XContig package scripts | ||
Revision as of 15:17, 25 October 2007
NCBI
seqin: standalone application
TA submission
AA submission
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
Use XContig package scripts
Files:
.contig, .seq, .qual, .ti2seq_name
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
* taxid: not recognized : replace <taxid>id</taxid> with <organism descriptor="TAXID">id</organism>
$ ls -1 umd-20070816-125223*
umd-20070816-125223.tar.gz
umd-20070816-125223/
1106158952778_stitched_20070817-141849.con # Contig consensus
1106158952778_stitched_20070817-141849.congap # Contig gaps
ASSEMBLY.xml # Assembly XML
MANIFEST # MD5 sums
3. validate: oXygen: software used by NCBI; license required xmllint: open source $ xmllint --schema ASSEMBLY.xsd umd-20070816-125223/ASSEMBLY.xml > /dev/null umd-20070816-125223/ASSEMBLY.xml validates