Xanthomonas oryzae

XCA : Xanthomonas campestris pv. armoraciae 756C

 JCVI 
 NCBI Taxonomy Tax ID: 329463

XOC : Xanthomonas oryzae pv. oryzicola BLS256; draft; NZ_AAQN00000000

 JCVI
 NCBI Taxonomy Tax ID: 129394

XOO : Xanthomonas oryzae pv. oryzae strain PXO99A

 JCVI
 NCBI Taxonomy Tax ID: 360094

 NCBI TA: 62,229 traces
 TA FTP

 NCBI AA 
   Location: /fs/szasmg/Bacteria/Xanthomonas/XOO/Xoo_PXO99A/FinalAsm_June2007/AA

   $ bank2contig Xoo.bnk/ > Xoo.contig
   $ grep ^# Xoo.contig | head
   ##1106158952778_stitched 62611 5249768 bases, 00000000 checksum.
   #XOOB626TF(-939) [] 998 bases, 00000000 checksum. {11 1004} <-938 59>
   #XO1EZ18TR(-764) [] 977 bases, 00000000 checksum. {19 993} <-763 213>
   ...   
   #XO1C975TF(5248807) [RC] 875 bases, 00000000 checksum. {891 19} <5239115 5239987>
   #XO1FR06TF(5248815) [] 952 bases, 00000000 checksum. {15 964} <5239123 5240072>

   $ bank2fasta -b Xoo.bnk/ > Xoo.fasta (5240073 bp , 63.63 GC%)

   Problem : seq_name's (Ex:XOOB626TF) must be mapped to trace_name's based on the .frg file
             trace_name's must be mapped to ti's based on anc. file
             => the .contig file must contain the ti's

   3,327 transposon & finishing traces not present in TA

   $ convertContig  --force-circ 1106158952778_stitched Xoo.translated.contig  
     ASSEMBY.xml

   # or

   $ test -f Xoo.contig Xoo.seq Xoo.qual
   $ makeConinfo Xoo.contig 
   $ buildAssemblyArchive Xoo.coninfo --prompt --subname umd-20070816-125223
     =>  tigr-20070816-125223.tar.gz
   $ ls -1 tigr-20070816-125223
     ASSEMBLY.xml
     MANIFEST                                       # MD5 sums
     1106158952778_stitched_20070816-125246.con     # Contig consensus
     1106158952778_stitched_20070816-125246.congap  # Contig gaps