Brugia malayi

Articles

• Science 2007
• Science 2007 Supplementary data

Genome Info

• 6 chromosomes: 1-5, XY
• ~ 90M, 30% GC, 32% coding, 15% repeats

Other sequences

• mitochondrion finished: 13,657 bp; 24% GC
• Wolbachia endosymbiont strain TRS from Brugia malayi strain wMel complete: 1,080,084 bp; 34%GC (New England Biolabs)
• Wolbachia endosymbiont strain wMel progress (TIGR)
• Rodent: some trace contamination; Example: Mus musculus is ~40%GC

Genome Project

• NCBI Genome project
• TIGR Genome project (TRS strain)
• NCBI AAQA00000000 AAQA01000001-AAQA01029808

 * 26,879 good ctgs
 * 2,929 jird contaminants (Example: AAQA01001321 : mouse 99%id hits)

 good ctg len
       #elem   min     max     mean    median  n50     sum
 all   26879   200     611244  3241    1005    19005   87119350
 10K+  1224    10036   611244  41018   23135   60727   50206329
 
 good ctg GC%
       #elem   min     max     mean    median  n50  
 all   26878   0.00    72.30   28.86   28.56   29.46
 10K+  1224    24.38   38.44   30.38   30.43   30.62

 contaminant ctg len
       #elem   min     max     mean    median  n50     sum
 all   2929    200     8994    740     675     763     2167588
 
 contaminant ctg GC%
       #elem   min     max     mean    median  n50  
 all   2929    18.09   75.96   44.1    43.59   44.80

Traces

 Libraries:
   * 2K : bulk of the sequence @TIGR
   * 15-20 K @TIGR
   * 8,000 BAC clones @Children's Hospital Oakland Research Institute.  (!!! no NCBI TA submission)

• NCBI TA
• NCBI TA FTP

Trace summary:

  * all:          1,260,215 
  * TRACE_TYPE_CODE 
    * WGS:        1,258,277 
    * TRANSPOSON:     1,437 
    * PRIMER_WALK       501
  * CENTER NAME
    * TIGR:         856,624
    * JCVI          403,591
  * NO BACS !!!; max INSERT_SIZE=23K

• TI's: 1172642810, ... ,1174845185
• SEQ_LIB_ID's : 1047111480027, ... , 1047174912885

FRG file:

• FRG.src : same as TI's above
• FRG.acc: 2 ..
• DST.acc: 1260217, ... , 1260234

Problems:

• All library insert sizes are underestimated
• The contaminant reads align at ~91-93% id to the contaminant ctgs while the Mt/We reads align at 99% id to Mt/We finished seq. What %id thold to use for contaminant?

Assemblies

TIGR

• 9X coverage, 856K Sanger traces => 8,200 scaff & 29,808 ctg (avg. scaff=~10K & avg ctg=~3K)
• "scaffolds totaling ~71 Mb of data with a further ~17.5 Mb of contigs not integrated into any scaffold (orphan contigs)" (Science 2007)

Files

 * /fs/szattic/asmg1/adelcher/Genomes/Brugia             : Art's files
 * /fs/sztmpscratch/cole/tarchive_download/brugia_malay  : Cole's files
 * /fs/szasmg3/dpuiu/Brugia_malayi/                      : Daniela's files