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

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: