Methanobrevibacter smithii

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Data

NCBI

1 complete + 2 draft assembly strains:

Methanobrevibacter smithii ATCC 35061

 cat NC_009515.gff | grep "IS%20element" | grep CDS | awk '{print $1,$2,$3,$4,$5,$6,$7,$5-$4+1}' 
 NC_009515.1    RefSeq  CDS  504499   505509   .  -  1011  
 NC_009515.1    RefSeq  CDS  505464   505748   .  -  285   
 NC_009515.1    RefSeq  CDS  508688   508984   .  +  297   
 NC_009515.1    RefSeq  CDS  509066   509491   .  +  426   
 NC_009515.1    RefSeq  CDS  509745   509900   .  +  156   
 NC_009515.1    RefSeq  CDS  1542734  1543111  .  -  378   
 NC_009515.1    RefSeq  CDS  1543120  1543254  .  -  135   
 NC_009515.1    RefSeq  CDS  1543220  1543417  .  -  198   
 ~/bin/RepeatSearch.amos -D REPEATLEN=36 ms
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 repeats.36+          317        36     43     63     104    3732       182.96     1363       57999          
 uniq.36+             309        1      24     109    2195   97573      5809.58    42534      1795160    

 repeats.350+         26         386    691    1386   1406   3732       1369.12    1390       35597          
 uniq.350+            25         1      13517  52288  90848  258405     72702.48   131389     1817562       

Methanobrevibacter smithii DSM 2374

  • draft: NZ_ABYV02000000
  • 1,727,775 bp
  • 25 contigs: NZ_ABYV02000001 .. NZ_ABYV02000025

Methanobrevibacter smithii DSM 2375

  • draft: NZ_ABYW00000000
  • 1,704,865 bp
  • 24 contigs: NZ_ABYW01000001 .. NZ_ABYW01000024

Methanobrevibacter smithii DSM 11975

  • progress

WUSTL (Gordon Lab)

 /fs/szattic-asmg4/methanobrevibacter_smithii/Data
  • 22 strains
  • half-way through sequencing (should have all the data by early to mid-January)
  • right now (--Dpuiu 15:19, 15 December 2009 (EST)):
    • 10 strains sequenced by GAII Illumina (36mers) with 3-8 million reads per strain (coverage is 50-150x),
    • 12 strains sequenced by 454-Titanium sequencing, with 20,000 to 90,000 reads per strain (coverage is ~5-20x).
    • 7 strains sequenced by Illumina and 454

Illumina: 36 bp single reads

   nl  strain      reads   bases       cvg
    1  FR1LH1      5186537 186715332   100
    2  FR1LH3      7211080 259598880   140
    3  FR1LH6      4968262 178857432   96
    4  TS145A      6536457 235312452   126
    5  TS145B      8277390 297986040   160
       TS146e4    26899427 968379372   522  # 8417021 of the reads (~ 160X cvg)  have qual==32
    6  TS94-3      4886376 175909536   94
    7  TS94-5      4785200 172267200   92
    8  TS95-2      2896065 104258340   56
    9  TS95-3      5064150 182309400   98
   10  TS95-4      3557512 128070432   69
   11  TS95-5      4559830 164153880   88

454: avg 342 bp single reads

   nl  strain      reads   bases       cvg
    1  TS145A      83667   28587141    15
    2  TS145B      45203   15720997    8
    3  TS146-3     49854   17608862    10
    4  TS146e4     58633   18306825    10
    5  TS146e5A    27844   8311560     4
    6  TS146e5B    73182   23547825    13
    7  TS147e8     68487   20662109    11
    8  TS94-3      449545  157306990   85
    9  TS94-5      76513   26734802    14
   10  TS95-2      73255   25779806    14
   11  TS95-4      85737   29231201    16
   12  TS95-5      96757   35000794    19

Illumina & 454 : 7 strands have both Illumina & 454 reads

                                Illumina                        454
                       ---------------------------     ---------------------------                             
   nl  strand          #reads  #bases          cvg     #read   #bases          cvg       avg%idFinishedGenome
    1  FR1LH1          5186537 186715332       100     .       .               .         98
    2  FR1LH3          7211080 259598880       140     .       .               .       
    3  FR1LH6          4968262 178857432       96      .       .               .       

    4* TS145A          6536457 235312452       126     83667   28587141        15        98
    5  TS145B          8277390 297986040       160     45203   15720997        8       
    6  TS146-3         .       .               .       49854   17608862        10
    7  TS146e4        26899427 968379372       522     58633   18306825        10
    8* TS146e5A        .       .               .       27844   8311560         4         98
    9  TS146e5B        .       .               .       73182   23547825        13
   10  TS147e8         .       .               .       68487   20662109        11

   11* TS94-3          4886376 175909536       94      449545  157306990       85        92
   12  TS94-5          4785200 172267200       92      76513   26734802        14
   13  TS95-2          2896065 104258340       56      73255   25779806        14
   14  TS95-3          5064150 182309400       98      .       .               .       
   15  TS95-4          3557512 128070432       69      85737   29231201        16
   16  TS95-5          4559830 164153880       88      96757   35000794        19
   nl  strand      IlluminaGC   454GC
    1  FR1LH1      38.89        .      
    2  FR1LH3      33.33        .      
    3  FR1LH6      33.33        .      

    4  TS145A      41.67        31.54  
    5  TS145B      36.11        31.52  
    6  TS146-3     .            31.85  
    7  TS146e4     33.33        31.72  
    8  TS146e5A    .            32.77  
    9  TS146e5B    .            31.96  
   10  TS147e8     .            31.11  

   11  TS94-3      30.56        30.67  
   12  TS94-5      30.56        30.69  
   13  TS95-2      36.11        30.60  
   14  TS95-3      33.33        .      
   15  TS95-4      30.56        30.70  
   16  TS95-5      33.33        30.56  

Based on nucmer alignments of finished genome and newbler contigs looks like

  • TS145A.4 & TS146e5A.8 99% id
  • TS145A.4 & TS94-3.11 92% id

Assembly

  • Available online at: ftp://ftp.cbcb.umd.edu/pub/data/dpuiu/Methanobrevibacter_smithii/
  • newbler assemblies are generally the "best": longer contigs, fewer 0cvg regions ...
  • CBCB velvet & newbler assemblies are slightly better than the WUSTL ones
  • velvet contigs slightly longer than the SOAPdenovo ones;
  • velvet assemblies contain slightly fewer bases than SOAPdenovo ones & have more 0cvg regions (compared to the reference)
  • can further merge the newbler(454) & velvet/SOAPdenovo(Illumina) assemblies; would merge some contigs together

AMOScmp.Illumina (CBCB)

               #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 FR1LH1.1      1684    36      55      109     650     33114   958     5106    1614205 275309
 FR1LH3.2      1642    36      55      106     631     33115*  984     5331    1616391 273301
 FR1LH6.3      1649    36      55      108     660     26387   979     5180    1615744 273654

 TS145A.4      1918    36      59      124     805     28850   838     3234    1608620 284953
 TS145B.5      1723    36      58      110     647     33114   936     4463    1612823 277233

 TS94-3.11     ??? 
 TS94-5.12     8859    36      56      85      155     10840   159     242     1408957 658124

 TS95-2.13     9535    36      55      82      147     7508    144     209     1380166 695098
 TS95-3.14     9152    36      56      85      154     10159   156     238     1436137 642175
 TS95-4.15     8859    36      56      85      155     10840   159     242     1408957 658124
 TS95-5.16     9238    36      55      84      152     10160   155     235     1435894 645655

SOAPdenovo.Illumina (CBCB)

               #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 FR1LH1.1      774     45      75      137     2158    50285   2353    10320   1821758 218968
 FR1LH3.2      767     45      73      108     977     56788*  2371    14018   1818948 221732
 FR1LH6.3      757     45      74      129     1396    50013   2402    12294   1818674 219385

 TS145A.4      1798    45      127     459     1381    13456   991     2225    1781905 230976
 TS145B.5      1098    45      83      306     2231    20523   1631    4869    1791302 216380

 TS94-3.11     1405    45      59      98      634     35690   1349    7940    1895871 249447
 TS94-5.12     1562    45      58      101     706     25048   1216    6456    1899512 251003

 TS95-2.13     6611    45      131     215     364     2994    281     375     1863491 404797
 TS95-3.14     1687    45      58      85      388     25368   1184    6931    1997443 213660
 TS95-4.15     1562    45      58      101     706     25048   1216    6456    1899512 251003
 TS95-5.16     1259    45      63      85      285     43875   1576    12739   1984835 209415

velvet.Illumina (CBCB)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 FR1LH1.1      518     45      73      158     3131    67401   3491    16101   1808646 219880
 FR1LH3.2      532     45      72      105     729     111372  3382    27042   1799368 227816
 FR1LH6.3      547     45      72      111     992     85069   3309    20751   1810235 220469

 TS145A.4      1002    45      398     1154    2228    14317   1575    2707    1578999 355737
 TS145B.5      687     45      105     773     3424    31627   2567    6873    1763953 223089

 TS146e4.7     375     45      71      129     1127    153113* 4740    40215   1777614 209640  # 522X cvg
 TS146e4.7.filt 7641   45      99      143     218     1244    177     207     1355197 626004  # 150X cvg (only q32 reads)

 TS94-3.11     738     45      63      102     755     99478   2526    17184   1864601 250197
 TS94-5.12     751     45      63      98      887     51451   2455    15583   1844453 259266

 TS95-2.13     7235    45      107     198     349     2547    265     370     1922674 382074
 TS95-3.14     1018    45      68      85      341     60536   1934    15001   1969398 211351
 TS95-4.15     751     45      63      98      887     51451   2455    15583   1844453 259266
 TS95-5.16     881     45      65      76      350     47906   2226    15468   1961518 212351

velvet.Illumina (WUSTL)

 strain        elem       min    q1     q2     q3     max        mean       n50        sum            
 FR1LH1.1      403        101    282    1950   5891   41268      4388       10473      1768436
 FR1LH3.2      274        100    267    1375   7601   88330*     6469       19398      1772541
 FR1LH6.3      291        100    224    1225   7594   84927      5768       17024      1678650

 TS145A.4      1127       101    409    1004   2075   11833      1479       2545       1667855
 TS145B.5      445        100    721    2392   4817   20558      3396       5896       1511226

 TS94-3.11     449        100    152    671    5121   50277      3958       12756      1777364
 TS94-5.12     468        100    154    634    4768   44436      3818       12667      1786983

 TS95-2.13     4476       100    179    303    531    3089       414        567        1853314
 TS95-3.14     484        100    186    725    5581   49558      3918       11725      1896543
 TS95-4.15     508        100    235    1211   5315   33145      3685       10173      1872243
 TS95-5.16     469        100    203    927    5304   42207      4038       12739      1894003

 MsmALI        209        102    371    3882   9790   58310      7882       21331      1647404
 MsmPS-copy    497        100    341    1399   4492   43636      3497       8361       1738127

AMOScmp.454 (CBCB)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 TS146e4.7     213     71      1454    3954    9800    62523   7725    15060   1645592 208920  # original reads 
 TS146e4.7     168     56      1312    4609    13025   62537   9908    24440   1664607 194003  # alignment trimmed reads

CA.bog.454 (CBCB)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 TS145A.4      39      1135    12340   37904   61833   166391  44902   83237   1751181 227444  
 TS146e4.7     111     1039    5766    11729   21286   105399  16055   22905   1782182 200113

newbler.deNovo.454 (CBCB)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 TS145A.4      48      131     883     9320    56233   210376  37056   112225  1778716 196515
 TS145B.5      117     104     2185    7850    22256   79935   15147   34389   1772299 203614

 TS146-3.6     441     100     248     398     497     106331  4295    37197   1894514 202108
 TS146e4.7     99      135     926     13013   24440   147105  17974   36272   1779476 198936
 TS146e5A.8    1183    98      326     770     1953    19970   1446    2812    1710725 350637
 TS146e5B.9    432     100     191     325     462     212980  4411    106361  1905607 195632

 TS147e8.10    86      132     1662    8952    35506   122338  22610   55697   1944471 221774

 TS94-3.11     723     96      238     361     456     395484* 2934    91958   2121818 224389
 TS94-5.12     67      103     778     5001    46879   173674  28164   82955   1887011 226423

 TS95-2.13     78      108     626     5843    45099   140027  25376   88829   1979337 187754
 TS95-4.15     58      111     387     11498   59591   169655  34241   89436   1986032 186252
 TS95-5.16     58      103     286     5198    59620   188214  34081   115574  1976737 186181

newbler.deNovo.454 (WUSTL)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 TS145A.4      62      106     386     3049    46046   166070  28692   82515   1778941
 TS145B.5      130     101     2104    7697    18636   79979   13620   34155   1770674

 TS146-3.6     384     100     349     447     1527    83020   4885    28235   1876197
 TS146e4.7     145     101     1901    7807    17092   73674   12238   24421   1774620
 TS146e5A.8    1199    100     591     932     1529    7108    1199    1566    1438364     much worse
 TS146e5B.9    112     111     490     1598    20451   129166  16084   52376   1801428

 TS147e8.10    136     100     1197    5950    17566   140484  14275   41840   1941435

 TS94-3.11     567     111     332     408     471     284245* 3642    93923   2065443
 TS94-5.12     87      130     375     1511    19610   189466  21686   71682   1886713

 TS95-2.13     78      116     350     8420    41426   136894  25419   73086   1982724
 TS95-4.15     60      112     373     2519    59614   200840  33056   115852  1983394
 TS95-5.16     50      132     463     20422   73626   191648  39557   89465   1977893

newbler.refMapper.454 (CBCB)

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 TS146e4.7     254     101     206     851     6803    72759   6408    25310   1627809 229435

best

Generated by merging newbler with velvet/SOAPdenovo contigs using minimus2

 strain        #ctgs   min     q1      q2      q3      max     mean    n50     sum     0cgv
 FR1LH1.1      169     47      307     3469    13513   113154  10746   29975   1816093 210847
 FR1LH3.2      159     47      162     2932    13757   113158  11288   37473   1794914 221522
 FR1LH6.3      157     50      269     3785    15911   126755  11603   29272   1821689 211256

 TS145A.4      48      131     883     9320    56233   210376  37056   112225  1778716 196515
 TS145B.5      53      71      1018    11425   57301   147750  33590   83876   1780320 198279

 TS146-3.6     441     100     248     398     497     106331  4295    37197   1894514 202108
 TS146e4.7     99      135     926     13013   24440   147105  17974   36272   1779476 198936
 TS146e5A.8    1183    98      326     770     1953    19970   1446    2812    1710725 350637
 TS146e5B.9    432     100     191     325     462     212980  4411    106361  1905607 195632

 TS147e8.10    86      132     1662    8952    35506   122338  22610   55697   1944471 221774

 TS94-3.11     38      55      764     9841    66968   395587  49738   144195  1890074 223341
 TS94-5.12     49      65      766     7044    51688   285237  38534   111850  1888200 225957

 TS95-2.13     57      110     1383    9455    50972   165660  34754   94352   1981005 182973
 TS95-3.14     408     47      141     419     5698    52172   4663    16369   1902753 202507
 TS95-4.15     79      47      147     2317    16017   200685  26493   138013  2092967 179552
 TS95-5.16     47      69      311     14482   77588   188308  42099   115630  1978688 184590

Strains

TS145A.4

  • 126x Illumina & 15x 454
 .                    elem       min    q1     q2     q3     max        mean       n50        sum         cvg      
 Illumina             6536457    36     36     36     36     36         36.00      36         235312452   126    
 454                  85737      30     247    377    453    626        340.94     422        29231201    15   
  • Read assemblies:
                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 AMOScmp.Illumina (soap2 -v5 -g0 -f2)        1918   36    59    124   805    28850   838    3234    1608620  284953  
 AMOScmp.Illumina (soap1 -v3 -g3 -f1 -c35)   1717   36    56    100   528    28868   964    4879    1656159  255687 
 SOAPdenovo.Illumina*                        1798   45    127   459   1381   13456   991    2225    1781905  230976  
 velvet.Illumina                             1002   45    398   1154  2228   14317   1575   2707    1578999  355737  

 AMOScmp.454                                 166    116   1110  3614  11776  110905  9952   24150   1652197  203385
 CA.454                                      203    1002  2802  6431  12196  41845   8646   13047   1755208  245426  
 newbler.454**                               48     131   883   9320  56233  210376  37056  112225  1778716  196515  
 SOAPdenovo.454                              6531   45    103   179   306    1806    237    321     1553899  478469  
 velvet.454                                  21165  45    53    65    83     548     73     74      1561277  821841  
 
 AMOScmp.Illumina_454(soap1 -v3 -g3 -f1 -c35) 274   36    46    86    4129   117510  6136   34524   1681406  186848
 SOAPdenovo.Illumina_454                     5795   45    75    184   425    3983    317    588     1840810  243391  
 velvet.Illumina_454                         4229   45    135   269   507    3529    384    584     1626062  396716

Contig assemblies(no singletons):

                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 minimus2.SOAPdenovo.Illumina-newbler.454    41     46    883   17898 61580  287497  43446  114143  1781287  197555  # 3 contigs don't contain any newbler original ctg
 minimus2.velvet.Illumina-newbler.454        36     289   1802  38243 70184  210459  49402  113849  1778497  197611  # all contigs contain at least 1 newbler original ctg

Contig assemblies(include singletons):

                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 minimus2.SOAPdenovo.Illumina-newbler.454    83     45    97    425   17898  287497  21689  114143  1800192  196885
 minimus2.velvet.Illumina-newbler.454        61     45    677   2956  43814  210459  29821  113849  1819092  197424

TS146e5A.8

  • 4x 454
  • Read assemblies:
                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 AMOScmp.454                                 736    56    675   1452  2902   17360   2092   3319    1540404  324145
 newbler.454*                                1183   98    326   770   1953   19970   1446   2812    1710725  350637

TS94-3.11

  • 94x Illumina & 85x 454
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 454                  449545     29     255    390    463    1190       349.92     433        157306990      
 Illumina             4886376    36     36     36     36     36         36.00      36         175909536
  • Read assemblies:
                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 SOAPdenovo.Illumina                         1405   45    59    98    634    35690   1349   7940    1895871  249447      
 velvet.Illumina                             738    45    63    102   755    99478   2526   17184   1864601  250197

 AMOScmp.454                                 255    52    585   2580  8321   61854   6531   16349   1665535  225050        
 newbler.454                                 723    96    238   361   456    395484  2934   91958   2121818  224389
 newbler.454.1000+                           44     1007  2480  9817  64051  395484  42923  106659  1888613
 CA.454                                      55     1001  1777  20479 51987  188883  34348  81660   1889177  244396        

newbler.454

  • ReadStatus counts
                       total  %
 Assembled             435637  96.91  
 Singleton             8178    1.82   
 PartiallyAssembled    4511    1      
 Outlier               856     0.19   
 Repeat                363     0.08   
 total                 449545  100
  • Location
 /fs/szattic-asmg4/methanobrevibacter_smithii/Assembly.CBCB/TS94-3.11/newbler.454/

CA.bog

 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 ctg                  55         1001   1777   20479  51987  188883     34348.67   81660      1889177        
 deg                  922        64     341    457    515    13313      460.62     489        424691  
  • Location
 /fs/szattic-asmg4/methanobrevibacter_smithii/Assembly.CBCB/TS94-3.11/CA.bog/