Brugia malayi: Difference between revisions

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   * 26,879 good ctgs
   * 26,879 good ctgs
   * 2,929 jird contaminants (Example: AAQA01001321 : mouse 99%id hits)
   * 2,929 jird contaminants (Example: AAQA01001321 : mouse 99%id hits)
 
* Stats
   good ctg len
   .                    elem       min    q1    q2    q3    max        mean      n50        sum             
      #ctgs       min    q1    q2    q3    max        mean      n50        sum             
   ctg.good            26879     200    836    1005  1495  611244*    3241.17    18986      87,119,350       
   all  26879       200    836    1005  1495  611244     3241.17    18986      871,19,350       
   ctg.good.2K+         4887       2000  2914  4380  10049  611244    13363.00  37130      65,304,988     
   2k+ 4887       2000  2914  4380  10049  611244    13363.00  37130      65,304,988     
    
    
   contaminant ctg len
   ctg.contaminant     2929       200    527    675    820    8994      740.04    762        2,167,588       
      #ctgs       min    q1    q2    q3    max        mean      n50        sum           
  all  2929        200    527    675    820    8994      740.04    762        2,167,588       


* Location  
* Location  
Line 255: Line 252:
* Date: 11/05/08
* Date: 11/05/08
* Stats:
* Stats:
        elem      min    q1    q2    q3    max        mean      n50        sum
                      elem      min    q1    q2    q3    max        mean      n50        sum
   scf   3170      2000  2917  4483  14471  6534162   22916      112914    72643770
   scf.2K+              3170      2000  2917  4483  14471  653416222916      112914    72,643,770


* Location:
* Location:

Revision as of 02:16, 16 February 2010

Articles

Genome Info

  • 6 chromosomes: 1-5, XY ; diploit genome ~ 110M bp
  • 30% GC,
  • 32% coding, 15% repeats

Other sequences

 contaminants       min    q1     q2     q3     max        mean       n50        sum            
 2929               200    527    675    820    8994       740.04     762        2167588

Genome Project

Brugia malayi has a diploid genome of approximately 110 Mb, organized in 6 pairs of chromosomes (five pairs of autosomes and one pair of sex chromosomes). In addition to the nuclear genome, B. malayi has a mitochondrial genome of about 14kb, and the genome of the harbored bacterial endosymbiont Wolbachia sp (1-2Mb).

The B. malayi genome project has been completed by The Institute for Genomic Research. Whole Genome Shotgun sequencing was used to obtain more than eight-fold coverage of the genome. The complete genome was assembled into approximately 8200 scaffolds and deposited in GenBank. The accession for the WGS project is AAQA00000000 and consists of sequences AAQA01000001-AAQA01029808. File location:

 /fs/szasmg3/dpuiu/Brugia_malayi/Data/Bm.fasta 
 ctgs               min    q1     q2     q3     max        mean       n50        sum            
 26879              200    836    1005   1495   611244     3241.17    18986      87119350   

Data

Original Traces

 SEQ_LIB_ID       INSERT_SIZE  INSERT_STDEV  TRACE_TYPE_CODE         
 1047113828118    1000         300           WGS              13500   
 1047113856575    1000         300           PRIMERWALK       325     
 1047111632737    1258         377           PRIMERWALK       3       
 1047111632737    1258         377           WGS              305,906  
 1047111540304    1415         424           WGS              51772   
 1047112577106    1415         424           WGS              337,789  
 1047111718946    3123         936           WGS              47597   
 1047113358719    3123         936           PRIMERWALK       173     
 1047113358719    3123         936           WGS              246,185  
 1047174912885    3123         936           TRANSPOSON       1437    
 1047113570927    6000         1800          WGS              3193    
 1047111814561    7158         2147          WGS              219,306  
 1047111480027    17168        5150          WGS              4087    
 1047111488095    17168        5150          WGS              3434    
 1047111495007    17168        5150          WGS              3716    
 1047111501919    17168        5150          WGS              3697    
 1047111480605    22419        6725          WGS              4638    
 1047111516154    22419        6725          WGS              4004    
 1047111523212    22419        6725          WGS              3766    
 1047111530126    22419        6725          WGS              5686    
 1047113855421    23000        6900          WGS              1       
 total                                                        1,260,215

FRG file:

  • FRG.src : TI's
  • FRG.acc: 2 ..
  • DST.acc: 1260217, ... , 1260234
  • Location
 /fs/szasmg3/dpuiu/Brugia_malayi/Data/nucmer_seq/Bm-all.frg 
 DST     15
 FRG     1178192
 LKG     530930
 
 seqs         min    q1     q2     q3     max        mean       n50        sum            
 1,178,192    65     645    771    850    1214       724        800        853,847,771  => 8X

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?

BACS

8,000 BAC clones @Children's Hospital Oakland Research Institute. (!!! no NCBI TA submission)

PITT FTP data

  • 3.21M 454 reads
  • 3K insert flx libraries (estimated to 2K based on alignment to the existing assembly)
  • 20K insert tit libraries (estimated to 28K ...)

CBCB Location:

 /fs/szattic-asmg4/brugia_malayi/Data/
 /fs/szattic-asmg4/brugia_malayi/Data/Sff/  # Sff files
 /fs/szattic-asmg4/brugia_malayi/Data/Frg/  # Frg files
 /fs/szattic-asmg4/brugia_malayi/Data/Seq/  # Seq files

FTP access:

 lftp -u bma 136.142.191.201
 pass: 6279
 user: bma
 # empty as of --Dpuiu 12:04, 8 January 2010 (EST)

Elodie's table:

 /scratch1/brugia_malayi/brugia-sequencing-summary.txt.csv
 #    elodie's date  protocol  platform  type            description                                run_name                                                                                                  Reads    Mates
 1    01/17/2008     WGS       Standard  Full run (2/2)  Mix of worms (calibration of the machine)  R_2008_01_31_18_01_35_FLX10070260_adminrig_ghedintestsample                                               ?        0
 2    07/01/2008     3Kb       Standard  Full            single worm (pUC contamination)            R_2008_08_06_13_52_29_FLX10070260_adminrig_080608_Ghedin-BrugiaLTPE1                                      492575   84341 
 3    09/11/2008     3kb       Standard  4/8 wells       single worm (pUC contamination)            R_2008_09_19_14_17_55_FLX10070260_adminrig_091908_HATFULL-MIDrepeat_GHEDIN-LTPE1                          263421   49258 
 4    10/01/2008     3Kb       Standard  Full            Mix of worms (still pUC contamination)     R_2008_10_14_15_06_50_FLX10070260_adminrig_101408_GHEDIN-Brugia-pool_LTPEtest                             59711    5096  
 5    02/01/2009     WGS       Standard  1/4 wells       Mix of worms; regions 2 & 3 were myxoma    R_2009_02_27_16_11_34_FLX10070260_adminrig_022709_GHEDIN                                                  ?        0
 6    04/06/2009     WGS       Standard  1/4 wells       Mix of worms; with comp. bio run           R_2009_04_15_14_46_56_FLX10070260_adminrig_041509_GHEDIN_r1-WGS1_r2-LMW4_r3-pool2compbio_r4-pool3compbio  ?        0
 7    05/01/2009     20Kb      Titanium  7/8 wells       Mix of worms                               R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1                              631287   213524
 8    10/28/2009     20Kb      Titanium  Full            Mix of worms                               R_2009_10_22_15_30_12_FLX10070260_adminrig_102209_GHEDIN_Brugia20kb2                                      1095713  377547
 9    Pending        3 Kb      Titanium  Full            Mix of worms                               ?                                                                                                         ?        ?
 .    Total                                                                                                                                                                                                   2542707  729766
  • 22 SFF files:
      run                                                                                                                                                                     sffReads  linker
 1    R_2008_01_31_18_01_35_FLX10070260_adminrig_ghedintestsample/D_2008_01_31_18_01_35_FLX10070260_adminrig_FullAnalysis/sff/E4RA0X101.sff                                     272923  .
 1    R_2008_01_31_18_01_35_FLX10070260_adminrig_ghedintestsample/D_2008_01_31_18_01_35_FLX10070260_adminrig_FullAnalysis/sff/E4RA0X102.sff                                     261899  .

 2    R_2008_08_06_13_52_29_FLX10070260_adminrig_080608_Ghedin-BrugiaLTPE1/D_2009_02_12_22_12_04_j_SignalProcessing/sff/FEZH5RS01.sff                                           228204  flx
 2    R_2008_08_06_13_52_29_FLX10070260_adminrig_080608_Ghedin-BrugiaLTPE1/D_2009_02_12_22_12_04_j_SignalProcessing/sff/FEZH5RS02.sff                                           264371  flx

 3    R_2008_09_19_14_17_55_FLX10070260_adminrig_091908_HATFULL-MIDrepeat_GHEDIN-LTPE1/FHAVB5T02.sff                                                                            86862   flx
 3    R_2008_09_19_14_17_55_FLX10070260_adminrig_091908_HATFULL-MIDrepeat_GHEDIN-LTPE1/FHAVB5T03.sff                                                                            87488   flx
 3    R_2008_09_19_14_17_55_FLX10070260_adminrig_091908_HATFULL-MIDrepeat_GHEDIN-LTPE1/FHAVB5T04.sff                                                                            89071   flx

 4    R_2008_10_14_15_06_50_FLX10070260_adminrig_101408_GHEDIN-Brugia-pool_LTPEtest/FIOXLOM01.sff                                                                               13695   flx
 4    R_2008_10_14_15_06_50_FLX10070260_adminrig_101408_GHEDIN-Brugia-pool_LTPEtest/FIOXLOM02.sff                                                                               14197   flx
 4    R_2008_10_14_15_06_50_FLX10070260_adminrig_101408_GHEDIN-Brugia-pool_LTPEtest/FIOXLOM03.sff                                                                               15515   flx
 4    R_2008_10_14_15_06_50_FLX10070260_adminrig_101408_GHEDIN-Brugia-pool_LTPEtest/FIOXLOM04.sff                                                                               16304   flx

 5    R_2009_02_27_16_11_34_FLX10070260_adminrig_022709_GHEDIN/FRLDXKV01.sff                                                                                                    18025   .

 6    R_2009_04_15_14_46_56_FLX10070260_adminrig_041509_GHEDIN_r1-WGS1_r2-LMW4_r3-pool2compbio_r4-pool3compbio/D_2009_04_16_14_19_21_morty_fullProcessing/FT9KOI001.sff         118490  .

 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY01.sff                           73807   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY02.sff                           91698   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY03.sff                           93878   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY04.sff                           90232   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY05.sff                           97065   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY06.sff                           94326   tit
 7    R_2009_06_05_16_18_41_FLX10070260_adminrig_060509_GHEDIN_Brugia-gDNA-TI20kb1/D_2009_06_08_15_32_36_compute-0-2_fullProcessing/sff/FW1OXFY07.sff                           90281   tit

 8    R_2009_10_22_15_30_12_FLX10070260_adminrig_102209_GHEDIN_Brugia20kb2/F4H5CMB01.sff                                                                                        551263  tit
 8    R_2009_10_22_15_30_12_FLX10070260_adminrig_102209_GHEDIN_Brugia20kb2/F4H5CMB02.sff                                                                                        544450  tit
 
      total                                                                                                                                                                     3214044 .
  • 22 Libraries
   lib          mean(orig)  mean(estimates) reads        mates   linker
 1 E4RA0X101    0           0               271066       0       .
 1 E4RA0X102    0           0               260166       0       .

 2 FEZH5RS01    3000        2000            181035       18676   flx
 2 FEZH5RS02    3000        2000            211064       22270   flx

 3 FHAVB5T02    3000        2000            68708        7850    flx
 3 FHAVB5T03    3000        2000            69306        8227    flx
 3 FHAVB5T04    3000        2000            70028        8353    flx

 4 FIOXLOM01    3000        0               10921        0       flx    # no mates !!!
 4 FIOXLOM02    3000        0               11157        0       flx    # no mates !!!
 4 FIOXLOM03    3000        0               12197        0       flx    # no mates !!!
 4 FIOXLOM04    3000        0               12727        0       flx    # no mates !!!

 5 FRLDXKV01    0           0               17349        0       .  

 6 FT9KOI001    0           0               108826       0       .

 7 FW1OXFY01    20000       28000           86127        15825   tit
 7 FW1OXFY02    20000       28000           106911       19668   tit
 7 FW1OXFY03    20000       28000           109874       20396   tit
 7 FW1OXFY04    20000       28000           104797       18933   tit
 7 FW1OXFY05    20000       28000           113716       20649   tit
 7 FW1OXFY06    20000       28000           110693       20326   tit
 7 FW1OXFY07    20000       28000           105931       19176   tit

 8 F4H5CMB01    20000       28000           626046       109918  tit
 8 F4H5CMB02    20000       28000           628432       118903  tit
 
   total        .           .               3297077      429170
 

Location:

 /fs/szattic-asmg4/brugia_malayi/Data/Frg/ 

 #clr of the seqs in the frg files
           seqs         min    q1     q2     q3     max        mean       n50        sum            
 all       3,297,077    3      156    248    301    2043       244        275        806,091,347 => 8X
 mated       858,340    64     107    156    223    612        171        201        147,070,298      
 unmated   2,438,737    2      207    261    335    2042       268        286        655,723,972

Contaminant search

nucmer -maxmatch -c 65 -l 40
          Sanger       454
 jird     31,501    197,420
 Mt        1,507      2,634
 We       49,014     23,249
 UniVec        ?    549,378    # most hits to "Cloning vector pBR322"

Assemblies

TIGR/NCBI

  • 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)
  • NCBI AAQA00000000 AAQA01000001-AAQA01029808
 * 26,879 good ctgs
 * 2,929 jird contaminants (Example: AAQA01001321 : mouse 99%id hits)
  • Stats
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 ctg.good             26879      200    836    1005   1495   611244*    3241.17    18986      87,119,350       
 ctg.good.2K+         4887       2000   2914   4380   10049  611244     13363.00   37130      65,304,988    
 
 ctg.contaminant      2929       200    527    675    820    8994       740.04     762        2,167,588       
  • Location
 /fs/szasmg3/dpuiu/Brugia_malayi/Assembly/TIGR/ <-> NCBI

CBCB

  • test wgs 5.1 on filtered Sanger reads
  • better assembly than the published one
  • Stats:
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 ctg                  12753      273    1245   1632   3873   376744     6113.39    24748      77,964,006       
 deg                  9661       65     858    949    1023   72494      1240.97    1008       11,988,997       
 scf                  10317      935    1215   1538   3462   3890532    8018.85    41716      82,730,474       

 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 ctg.2K+              5210       2000   3049   4813   13528  376744     13013.29   30835      67,799,238       
 deg.2K+              391        2000   3009   4693   10099  72494      8104.38    12352      3,168,812        
 scf.2K+              3656       2001   3181   5733   18904  3890532    20189.57   50293      73,813,083       

 reads                1178192(100%)
 singletons           134119 (11.43%)
  • Location:
 /fs/szasmg3/dpuiu/Brugia_malayi/Assembly/CBCB/2008_0826_CA/

PITT

  • Best so far
  • Date: 11/05/08
  • Stats:
                      elem       min    q1     q2     q3     max        mean       n50        sum
 scf.2K+              3170       2000   2917   4483   14471  6534162*   22916      112914     72,643,770
  • Location:
 /fs/szasmg3/dpuiu/Brugia_malayi/Assembly/PITT/

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

 /scratch1/brugia_malayi/Data/                         : ftp PITT data
 /fs/szattic-asmg4/brugia_malayi                       : ftp PITT data (as well)