Methanobrevibacter smithii

Data

NCBI

1 complete + 2 draft assembly strains:

Methanobrevibacter smithii ATCC 35061

• complete: NC_009515.1
• 1,853,160bp
• Ref: /fs/szdata/ncbi/ftp.ncbi.nih.gov/genomes/Bacteria/Methanobrevibacter_smithii_ATCC_35061/*fna
• Published: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut PNAS
• Assembled: Phrap and PCAP
• Repeats.png

 min%identity         elem       min    q1     q2     q3     max        mean       n50        sum            
 94                   70         1102   1360   1383   1393   1408       1373       1383       96142          
 99                   66         1358   1363   1383   1394   1408       1381       1383       91155          

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)

• Ftp:

 http://cgsweb.wustl.edu/~hansene/

• Location:

 /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).

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
    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

   nl  strand          #reads  #bases          cvg     #read   #bases          cvg       avg%idFinishedGenome
    1  FR1LH1          5186537 186715332       100     .       .               .
    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         .       .               .       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

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

• TS145A.4 & TS146e5A.8 99% id
• TS145A.4 & TS94-3 92% id

TS145A.4

Read assemblies:

                                            #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 AMOScmp.Illumina                           1918   36    59    124   805    28850   838    3234    1608620  284953  
 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                                 135    114   1012  4414  12554  110913  12255  36870   1654428  203524  
 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  

 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

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

Read assemblies:

                                             #ctgs  min   q1    q2    q3     max     mean   n50     sum      0cgv
 SOAPdenovo.Illumina                         1405   45    59    98    634    35690   1349   7940    1895871  249447      
 AMOScmp.454                                 255    52    585   2580  8321   61854   6531   16349   1665535  225050       

 newbler.454                                 723    96    238   361   456    395484  2934   91958   2121818  224389