Helicobacter pylori

Data

Wustl

• http://gordonlab.wustl.edu/MengWu/WU_JBC_2009.html
• http://pathogenomics.bham.ac.uk/blog/2009/09/tips-for-de-novo-bacterial-genome-assembly/
• http://www.jbc.org/content/early/2009/09/01/jbc.M109.052738.abstract

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

• Alignment info (NC_000915 0cvg regions)

       .                      elem  min  q1   q2   q3   max    mean  n50   sum
    1  NC_000915-NC_000915    .     .    .    .    .    .      .     .     .
    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

NCBI SRA

• http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&term=SRP001104 (24 data sets; 10 not loaded)
• http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP001104

Assemblies

Wustl

    .  .                                                    ctgs  min  q1   q2    q3     max    mean  n50    sum       reads     
    1  HPKX_1039_AG0C1.scarf.assembled-29-21                233   100  318  1700  9639   77743  7085  19912  1650899   0
    2  HPKX_1039_AG0C2.solexa.txt.assembled-23-12           420   101  341  1684  5301   36588  3914  9412   1644043   5.2M
    3  HPKX_1039_AG4C1.scarf.assembled-27-22                271   100  217  1421  8273   90368  6115  17093  1657230   0
    4  HPKX_1039_AG4C2.solexa.txt.assembled-25-12           365   100  301  1595  5658   51523  4522  11890  1650547   6.8M
    5  HPKX_1172_AG0C1_090424.solexa.txt.assembled-25-30    217   107  557  3370  10683  58848  7099  15527  1540507   8.6M
    6  HPKX_1172_AG0C2_2lanes.assembled-21-8                1170  100  264  717   1768   11444  1319  2661   1543511   7.2M
    7  HPKX_1172_AG4C1_090424.solexa.txt.assembled-23-20    377   103  355  2178  6166   35180  4169  9160   1571948   8.5M
    8  HPKX_1172_AG4C2.solexa.txt.assembled-25-15           317   100  274  1540  6256   37505  4987  14946  1581161   6.0M
    9  HPKX_1259_NL0C1.scarf.assembled-21-17                1704  100  264  598   1274   7953   936   1606   1595297   0  
   10  HPKX_1259_NL0C2.solexa.txt.assembled-23-12           410   102  240  928   4863   32792  3882  11295  1591864   3.6M
   11  HPKX_1259_NL4C1.scarf.assembled-27-23                283   100  224  1098  6814   98400  5634  18624  1594699   0
   12  HPKX_1259_NL4C2.solexa.txt.assembled-23-12           455   102  222  874   4348   32792  3520  11010  1601950   6.3M
   13  HPKX_1379_NL0C1.scarf.assembled-27-22                295   100  230  1243  7551   59556  5539  15858  1634019   0
   14  HPKX_1379_NL0C2.solexa.txt.assembled-23-12           416   100  216  1000  5177   53581  3931  11219  1635644   6.3M
   15  HPKX_1379_NL4C1.scarf.assembled-25-23                328   100  227  1084  6601   61090  4996  14203  1638925   0
   16  HPKX_1379_NL4C2.solexa.txt.assembled-25-20           291   100  231  1501  6751   64227  5539  15080  1612046   4.6M
   17  HPKX_345_AG4C1.scarf.assembled-27-22                 251   100  241  1272  8265   97643  6534  19718  1640151   0
   18  HPKX_345_NL0C1.scarf.assembled-25-30                 305   100  243  1146  6718   59632  5360  15874  1634815   0
   19  HPKX_345_NL0C2_090424.solexa.txt.assembled-25-26     283   100  254  2009  8300   59229  5629  13524  1593064   11.1M
   20  HPKX_438_AG0C1.scarf.assembled-27-25                 267   100  348  1710  8311   87876  6071  16918  1620975   0M
   21  HPKX_438_AG0C2.solexa.txt.assembled-23-18            407   102  396  1777  5455   31183  3963  8830   1613167   6.3M
   22  HPKX_438_CA4C1.scarf.assembled-27-26                 237   100  348  1580  8856   97139  6845  19582  1622487   0
   23  HPKX_438_CA4C2.solexa.txt.assembled-23-11            485   101  363  1502  4408   35471  3332  7779   1616183   4.1M
   24  HPKX_345_AG4C2                                       .                                                          12.1M

CBCB

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

Velvet:

1. Fastq vs Fasta: no diffrence
2. "velvetg . -exp_cov 80" vs "velvetg . -exp_cov auto" slightly worse

Kmers:

 meryl -C -B -m 12 -s prefix.seq -o prefix.12mers
 meryl -Dh -s prefix.12mers | sort -nk2 -r | more