Helicobacter pylori: Difference between revisions

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     16    HPKX_1379_NL4C2                                    167  101  262  1511  13732  95996  9720  32534  1623349
     16    HPKX_1379_NL4C2                                    167  101  262  1511  13732  95996  9720  32534  1623349
   
   
     18    HPKX_345_AG4C2                                    751  101  416  1129  2583  24913  2025  3967  1520951  # still not that good
     18    HPKX_345_AG4C2                                    751  101  416  1129  2583  24913  2025  3967  1520951  # still not that good; could try the method used for assembly 6 HPKX_1172_AG0C2
     20    HPKX_345_NL0C2                                    208  101  239  1581  10973  87982  7862  23967  1635408
     20    HPKX_345_NL0C2                                    208  101  239  1581  10973  87982  7862  23967  1635408
   
   

Revision as of 20:20, 23 October 2009

Data

Wustl

NCBI complete genomes

  • Genome info
       id             len     gc%
    1  NC_000915.1    1667867 38.87  Helicobacter pylori 26695
    2  NC_000921.1    1643831 39.19  Helicobacter pylori J99
    3  NC_008086.1    1596366 39.08  Helicobacter pylori HPAG1
    4  NC_010698.2    1608548 38.91  Helicobacter pylori Shi470
    5  NC_011333.1    1652982 38.89  Helicobacter pylori G27
    6  NC_011498.1    1673813 38.81  Helicobacter pylori P12
    7  NC_012973.1    1576758 39.16  Helicobacter pylori B38
  • nucmer -c 40 => ~200 alignments & 93-95% identity between genomes
  • SNPs are mostly substitutions
  • Alignment info (NC_000915 0cvg regions) :5-10% of genomes are unique
       .                      elem  min  q1   q2   q3   max    mean  n50   sum
    1  NC_000915-NC_000915    72    45   178  294  1890 10467  1013  1893  72976   #longest alignment has been removed
    2  NC_000915-NC_000921    197   2    81   203  495  17816  644   2146  126988
    3  NC_000915-NC_008086    151   3    103  242  894  26862  951   3103  143652
    4  NC_000915-NC_010698    206   2    115  283  706  12779  726   1941  149744
    5  NC_000915-NC_011333    138   2    111  260  695  7457   688   1941  95063
    6  NC_000915-NC_011498    157   2    83   185  565  5362   505   1357  79337
    7  NC_000915-NC_012973    140   2    108  239  526  37389  1018  5729  142568
  • NC_000915 vs NC_000915 : nucmer -c 40
 Align len
.                   elem       min    q1     q2     q3     max        mean       n50        sum
nucmer -c 20        484        20     21     26     82     10467      196        1892       95007
nucmer -c 40        72         45     178    294    1890   10467      1013       1893       72976
 Align %id
.                   elem       min    q1     q2     q3     max        mean       n50        sum
-c 20               484        63.72  91.89  100.00 100.00 100.00     95         100        46014.71
-c 40               72         76.71  85.06  92.86  99.92  100.00     92         93         6639.6
 Media:NC 000915-NC 000915.20.png, Media:NC 000915-NC 000915.40.png

NCBI SRA

Other

Assemblies

Wustl

velvet contigs 100bp+ stats:

   nl    assembly                                           ctgs  min  q1   q2    q3     max    mean  n50    sum      reads  0cvg   
   1     HPKX_1039_AG0C1.scarf.assembled-29-21              233   100  318  1700  9639   77743  7085  19912  1650899  6.4m   674288   
   2     HPKX_1039_AG0C2.solexa.txt.assembled-23-12         420   101  341  1684  5301   36588  3914  9412   1644043  5.2M   729736   
   3     HPKX_1039_AG4C1.scarf.assembled-27-22              271   100  217  1421  8273   90368  6115  17093  1657230  6.0m   687296   
   4     HPKX_1039_AG4C2.solexa.txt.assembled-25-12         365   100  301  1595  5658   51523  4522  11890  1650547  6.8M   708607   

   5     HPKX_1172_AG0C1_090424.solexa.txt.assembled-25-30  217   107  557  3370  10683  58848  7099  15527  1540507  8.6M   1068848  
   6     HPKX_1172_AG0C2_2lanes.assembled-21-8              1170  100  264  717   1768   11444  1319  2661   1543511  7.2M   1110550  95.8%id to HP_HPAG1
   7     HPKX_1172_AG4C1_090424.solexa.txt.assembled-23-20  377   103  355  2178  6166   35180  4169  9160   1571948  8.5M   1106858  
   8     HPKX_1172_AG4C2.solexa.txt.assembled-25-15         317   100  274  1540  6256   37505  4987  14946  1581161  6.0M   812671   

   9     HPKX_1259_NL0C1.scarf.assembled-21-17              1704  100  264  598   1274   7953   936   1606   1595297  4.2m   963211   
   10    HPKX_1259_NL0C2.solexa.txt.assembled-23-12         410   102  240  928   4863   32792  3882  11295  1591864  3.6M   824474   
   11    HPKX_1259_NL4C1.scarf.assembled-27-23              283   100  224  1098  6814   98400  5634  18624  1594699  6.4m   797825   
   12    HPKX_1259_NL4C2.solexa.txt.assembled-23-12         455   102  222  874   4348   32792  3520  11010  1601950  6.3M   833155   

   13    HPKX_1379_NL0C1.scarf.assembled-27-22              295   100  230  1243  7551   59556  5539  15858  1634019  6.1m   730236   
   14    HPKX_1379_NL0C2.solexa.txt.assembled-23-12         416   100  216  1000  5177   53581  3931  11219  1635644  6.3M   754915   
   15    HPKX_1379_NL4C1.scarf.assembled-25-23              328   100  227  1084  6601   61090  4996  14203  1638925  5.0m   716540   
   16    HPKX_1379_NL4C2.solexa.txt.assembled-25-20         291   100  231  1501  6751   64227  5539  15080  1612046  4.6M   785276   

   17    HPKX_345_AG4C1.scarf.assembled-27-22               251   100  241  1272  8265   97643  6534  19718  1640151  4.5m   727208   
   18    HPKX_345_AG4C2                                     .     .    .    .     .      .      .     .      .        12.1M  .
   19    HPKX_345_NL0C1.scarf.assembled-25-30               305   100  243  1146  6718   59632  5360  15874  1634815  5.7m   759194   
   20    HPKX_345_NL0C2_090424.solexa.txt.assembled-25-26   283   100  254  2009  8300   59229  5629  13524  1593064  11.1M  1067288  

   21    HPKX_438_AG0C1.scarf.assembled-27-25               267   100  348  1710  8311   87876  6071  16918  1620975  5.8m   755933   
   22    HPKX_438_AG0C2.solexa.txt.assembled-23-18          407   102  396  1777  5455   31183  3963  8830   1613167  6.3M   804474   
   23    HPKX_438_CA4C1.scarf.assembled-27-26               237   100  348  1580  8856   97139  6845  19582  1622487  6.0m   742559   
   24    HPKX_438_CA4C2.solexa.txt.assembled-23-11          485   101  363  1502  4408   35471  3332  7779   1616183  4.1M   801123

CBCB

velvet contigs 100bp+ stats:

   nl    assembly                                           ctgs  min  q1   q2    q3     max    mean  n50    sum      reads  0cvg      qual   comment
   2     HPKX_1039_AG0C2                                    417   101  730  2132  5402   34482  3937  8041   1642106  2.9M   722358    q28    little worse
   4     HPKX_1039_AG4C2                                    250   100  287  2134  9314   90459  6604  18459  1651103  6.7M   703430    q00     
   
   5     HPKX_1172_AG0C1                                    213   100  229  1521  9559   93714  7423  22783  1581145  7.1M   795376    q20     
   6*    HPKX_1172_AG0C2                                    1122  100  466  900   1639   7935   1243  1857   1395595  3.1M   1915029   q30    worse     
   7     HPKX_1172_AG4C1                                    313   100  373  2061  7176   67930  5131  13160  1606127  6.0M   811067    q30     
   8     HPKX_1172_AG4C2                                    218   102  280  1561  10678  79935  7225  22481  1575172  5.1M   802832    q20     
   
   10    HPKX_1259_NL0C2                                    271   102  296  1687  7254   78486  5869  17821  1590749  3.1M   811063    q20    
   12    HPKX_1259_NL4C2                                    311   101  214  901   6216   78488  5137  17546  1597850  5.5M   816013    q20    
   
   14    HPKX_1379_NL0C2                                    237   101  213  1039  8905   79512  6874  22931  1629236  3.9M   744144    q20    
   16    HPKX_1379_NL4C2                                    230   101  225  1440  9348   79083  7055  21887  1622754  4.8M   742039    q20     
   
   18    HPKX_345_AG4C2                                     1130  101  389  846   1732   14790  1349  2295   1525450  6.5M   1283074   q20    missing  
   20    HPKX_345_NL0C2                                     260   101  216  1515  8697   59766  6286  18718  1634563  9.1M   750135    q20     
    
   22    HPKX_438_AG0C2                                     272   102  433  2271  7395   53896  5945  14906  1617041  4.7M   768889    q20     
   24    HPKX_438_CA4C2                                     356   102  432  2029  6132   36335  4546  11461  1618724  3.0M   775835    q20     

 Files:  
    /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_*/velvet/

velvet-merged contigs 100bp+ stats: (merged based on alignments to the 7 complete genomes) ; minOVL=5bp

   nl    assembly                                           ctgs  min  q1   q2    q3     max    mean  n50    sum      
   2     HPKX_1039_AG0C2                                    230   101  575  2665  10199  81516  7129  17062  1639841
   4     HPKX_1039_AG4C2                                    192   100  318  2402  12716  95840  8601  21767  1651530

   5     HPKX_1172_AG0C1                                    161  100   229  1602  13093  98369  9826  33745  1582047
   6     HPKX_1172_AG0C2                                    275  100   774  2840  7251   45605  5732  12775  1576564   # merged AMOScmp(6**) and velvet(6*) contigs; did not use the complete genomes for alignments minOVL=40bp
   7     HPKX_1172_AG4C1                                    204  103   415  2527  12920  76550  7865  19077  1604640
   8     HPKX_1172_AG4C2                                    183  102   256  1344  13094  79936  8612  25128  1576072
 
   10    HPKX_1259_NL0C2                                    198  102   296  1152  10414  91140  8036  24879  1591324
   12    HPKX_1259_NL4C2                                    255  101   216  729   8686   78488  6272  20602  1599364
 
   14    HPKX_1379_NL0C2                                    183  101   226  1039  11932  96425  8912  32446  1630904
   16    HPKX_1379_NL4C2                                    167  101   262  1511  13732  95996  9720  32534  1623349

   18    HPKX_345_AG4C2                                     751  101   416  1129  2583   24913  2025  3967   1520951  # still not that good; could try the method used for assembly 6 HPKX_1172_AG0C2
   20    HPKX_345_NL0C2                                     208  101   239  1581  10973  87982  7862  23967  1635408

   22    HPKX_438_AG0C2                                     198  102   393  2767  10090  96481  8165  23774  1616761
   24    HPKX_438_CA4C2                                     224  102   433  2320  10298  53648  7220  19679  1617399

 Files:  
    /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_*/velvet/minimus3/
    /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_*/minimus2/

AMOScmp contigs 100bp+ stats:

    nl    assembly                                          ctgs  min  q1   q2    q3     max    mean  n50    sum      reads  0cvg     qual   comment
    2     HPKX_1039_AG0C2                                   286   100  341  2402  8354   90182  5718  12867  1635626  4.7M   .        q00    HPKX_1039_AG4C2 ref

    6**   HPKX_1172_AG0C2                                   367   100  300  1727  5675   37710  4294  10457  1575949  5.5M   .        q00    HPKX_1172_AG0C1 ref
 Files:  
    /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_*/AMOScmp

velvet_0.7.55:

  1. Fastq vs Fasta: no diffrence
  2. velvetg . -exp_cov auto

6 HPKX_1172_AG0C2

Reads:

  • all : 7.1M
  • q30+: 3.1M
  • aligned by soap Helicobacter pylori HPAG1 : 4.8M
  • aligned by soap Helicobacter pylori HPKX_1172_AG0C1 : 5.5M

velvet

 .               elem     min  q1   q2   q3    max    mean  n50   sum        reads  0cvg     qual  
 ctgs            1239     45   346  799  1528  7935   1132  1834  1403538    3.1M   1889408  q30   
 ctgs.100+       1122     100  466  900  1639  7935   1243  1857  1395595    3.1M   1915029  q30  

AMOScmp-shortReads (ref HP_HPAG1)

 .               elem     min  q1   q2   q3    max    mean  n50   sum        reads  0cvg     qual
 ctgs.all        1334     36   78   238  1283  16118  1146  3978  1529868    4.8M   1137259  q00
 ctgs.100+       905      100  223  728  2152  16133  1662  4073  1504146    .      .        q00

Directory:

 /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_1172_AG0C2.6/AMOScmp.HP_HPAG1

AMOScmp-shortReads (ref 5 HPKX_1172_AG0C1)

 .               elem     min  q1   q2   q3    max    mean  n50   sum        reads  0cvg     qual
 ctgs.all        392      37   227  1470 5481  37710  4024  10457 1577557    5.5M   .        q00
 ctgs.100+       367      100  300  1727 5675  37710  4294  10457 1575949
 
 ref             213      100  229  1521 9559  93714  7423  22783 1581145

Directory:

 /fs/szasmg3/dpuiu/Helicobacter_pylori/HPKX_1172_AG0C2.6/AMOScmp.HPKX_1172_AG0C1

18 HPKX_345_AG4C2

Reads

  • 12.1M Solexa 36bp unpaired
  • cvg =~ 120X ?

Velvet

Ctg stats :

 hash  #ctgs    min  q1   q2    q3    max    mean  n50    sum
 23    1098     45   244  724   1799  25718  1367  2745   1501014

24 HPKX_438_CA4C2.solexa.txt.assembled-23-11

Reads

  • 4.1M Solexa 36bp unpaired
  • cvg =~ 80X
  • ~9% of the reads contain at least one N

Quality QC:

 .                  elem                                  min    q1     q2     q3     max        mean       n50        sum
 Ncount             4107397    3725799<=0    381598>0     0      0      0      0      35         1          34         5614614
 avgQuality         4107397    118980<=20    3988417>20   0      19     26     29     34         22         28         91690471
 Ncount==0 and avgQuality>=20 => 3013939 filtered reads (73%)
 pos                  elem       min    q1     q2     q3     max        mean       n50        sum
 0                    4107397    0      32     33     33     33         28         33         116108100
 1                    4107397    0      30     33     34     34         27         33         114845690
 5                    4107397    0      27     32     33     34         26         33         109832819
 10                   4107397    0      23     31     33     34         25         32         102860584
 20                   4107397    0      17     28     31     34         22         30         92139539
 30                   4107397    0      2      21     28     34         17         27         70231217
 32                   4107397    0      2      19     26     34         15         26         63156733
 35                   4107397    0      2      2      25     34         13         26         55261361

12mer counts: too much error???

 meryl -C -B -m 12 -s prefix.seq -o prefix.12mers
 meryl -Dh -s prefix.12mers | sort -nk2 -r | more
 1       1876075 0.3452  0.0196
 2       1009161 0.5308  0.0407
 ...
 9       36227   0.7772  0.1017
 10      25866   0.7819  0.1044
 48      20812   0.8729  0.2727  # read cvg ??? 
 49      20726   0.8768  0.2833
 ...

Velvet (all reads)

Ctg stats for different velveth hash_lengths:

 hash  #ctgs    min  q1   q2    q3    max    mean  n50    sum
 19    908      37   161  770   2289  21014  1732  3905   1572704
 21    457      41   84   580   4156  49037  3548  12777  1621652
 23    398      45   161  1435  5137  37278  4068  12278  1619323  (CBCB best*)
 27    769      53   341  1163  2731  18704  2109  4319   1622389

 ?     485      101  363  1502  4408  35471  3332  7779   1616183  (WUSTL)

CBCB best* read cvg =~ 23; repeats at higher cvg

 .     #ctgs    min  q1   q2    q3    max    mean  n50    sum
 cvg   398      13   21   23    25    139    30    25     .

Velvet (filtered reads)

Hash_len=23

Ctg stats

 filter           #ctgs    min  q1   q2    q3    max    mean  n50    sum          #reads     0cvg(all 6 genomes)
 all              398      45   161  1435  5137  37278  4068  12278  1619323      4107397    765345
 noN              420      45   115  1194  4898  37173  3863  11880  1622651      3725799    759343
 avgqual20+       424      45   150  1302  4797  36335  3828  11749  1623136      3069665    757697 
 noN.avgqual20+   453      45   137  1093  4394  36335  3586  11461  1624653      3013939    756829     !!! least seq missing

AMOScmp

Ref : NC_000915

Ctg stats:

 params                           #ctgs      min    q1     q2     q3     max        mean       n50        sum       #readsInCtgs
 -l 16 -c 32 -ovl 10              9533       36     59     96     168    3160       136        185        1302448   1,123,025 (~25%) 1,023,929:0SNP 154,958:1SNP 8,532:2SNP ...
 -l 8  -c 24 -ovl 10              4429       36     62     152    430    5518       350        806        1554095   2,438,762 (~50%) 1,159,669:0SNP 977,687:1SNP 422,738:2SNP ...
 -l 8  -c 24 -ovl 5               3880       36     61     158    492    5883       400        966        1553027   2,438,762 (~50%)

nucmer 0cvg stats:

params                            #gaps      min    q1     q2     q3     max        mean       n50        sum 
 -l 16 -c 32                      8708       2      10     19     41     9286       44         91         388608 
 -l 8  -c 24                      2650       2      8      17     45     2347       56         207        150099

NC_011498

NC_011498.1 1673813 38.81

Reads

  • 1.67M Simulated reads 36bp; unpaired; 100% correct;
  • the reads were generated by breaking the genome in 36bp segments (35bp ovl)=>36X cvg

Velvet

  • Ctg stats :
 hash                     #ctgs    min  q1   q2    q3    max    mean  n50    sum
 23                       292      45   67   164   3422  73108  5654  33268  1651121

Euler-sr

  • Ctg stats :
 vertex_size              #ctgs    min  q1   q2    q3    max    mean  n50    sum        #misassemblies  0cvg
 23                       366      24   36   92    931   83748  4596  41745  1682410    . 
 25                       343      26   39   98    1125  83752  5075  42087  1740988    4               27377
 27                       331      28   43  109    1125  83756  5016  41753  1660506    4               27392

AMOScmp

  • Ref : NC_000915
  • Ctg stats:
 params                                   #ctgs    min  q1   q2    q3    max    mean  n50    sum        #readsInCtgs    misassemblies(<95%length match)
 nucmer -l 16 -c 32 -ovl 10               8569     36   66   114   203   2897   164   231    1405371    836827  (~50%)  39 
 soap -v 5 -g 3 -s 12 -f 2; -ovl 10       1787     37   99   305   1129  14043  881   2283   1574554    1437078 (~85%)  69
 soap -v 5 -g 0 -s 12 -f 2; -ovl 10       1789     37   98   304   1128  14043  880   2283   1574516    1437077         64
 soap -v 3 -g 0 -s 12 -f 2; -ovl 10       3646     36   89   214   532   7184   424   857    1548982                    55
 soap -v 3 -g 0 -s 12 -f 2; -ovl 20       4957     36   81   174   389   4783   316   580    1567357    1353104         49
  • 0cvg stats
 params                                   #gaps    min  q1   q2    q3    max    mean  n50    sum
 nucmer -l 16 -c 32 -ovl 10               8026     2    8    15    34    5384   36    75     291959
 soap -v 5 -g 3 -s 12 -f 2; -ovl 10       1042     2    6    19    46    5355   93    746    97176

minimus* on velvet contigs

 .                                    ctgs       min    q1     q2     q3     max        mean       n50        sum            
 velvet                               292        45     67     164    3422   73108      5654       33268      1651121      
                                      ctgs+sing  min    q1     q2     q3     max        mean       n50        sum      misas.
 minimus2(delta-filter -1; OVL=20)    191        45     108    465    10421  117862     8631       33268      1648580  17(6)  # ctgs-vs-ctgs; OVL=20
 minimus3(delta-filter -q; OVL=20)    251        45     68     214    5486   73108      6573       33268      1650065  11()   # ctgs-vs-ref => ctgs-vs-ctgs
 minimus3(delta-filter -q; OVL=5)     191        45     71     227    9222   73108      8631       41743      1648698  6(1)
 minimus3(                OVL=20)     204        45     115    560    10394  117862     8072       33268      1646865  5(1)
 minimus3(                OVL=5)      172        45     134    611    12957  122309     9572       37367      1646538  8(4) 
 minimus3(all ref; OVL=20)            231        45     99     357    7424   117862     7138       33268      1648917  5(1)
 minimus3(all ref; OVL=5)             150        45     140    1177   15439  118850     10959      41743      1643998  15(7)