Methanobrevibacter smithii: Difference between revisions
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* Published: [http://www.pnas.org/content/104/25/10643.long Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut] PNAS | * Published: [http://www.pnas.org/content/104/25/10643.long Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut] PNAS | ||
* Assembled: Phrap and PCAP | * Assembled: Phrap and PCAP | ||
* Repeats | * [[Media:methanobrevibacter_smithii.1con-1con.png|Repeats.png]] | ||
min%identity elem min q1 q2 q3 max mean n50 sum | min%identity elem min q1 q2 q3 max mean n50 sum | ||
94 70 1102 1360 1383 1393 1408 1373 1383 96142 | 94 70 1102 1360 1383 1393 1408 1373 1383 96142 | ||
Revision as of 17:20, 18 December 2009
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
1 FR1LH1 5186537 186715332 100 . . .
2 FR1LH3 7211080 259598880 140 . . .
3 FR1LH6 4968262 178857432 96 . . .
4* TS145A 6536457 235312452 126 83667 28587141 15
5* TS145B 8277390 297986040 160 45203 15720997 8
6 TS146-3 . . . 49854 17608862 10
7 TS146e4 . . . 58633 18306825 10
8 TS146e5A . . . 27844 8311560 4
9 TS146e5B . . . 73182 23547825 13
10 TS147e8 . . . 68487 20662109 11
11* TS94-3 4886376 175909536 94 449545 157306990 85
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
TS145A.4
Illumina read assemblies:
#ctgs min q1 q2 q3 max mean n50 sum 0cgv AMOScmp 1918 36 59 124 805 28850 838 3234 1608620 284953 SOAPdenovo* 1798 45 127 459 1381 13456 991 2225 1781905 230976 velvet 1002 45 398 1154 2228 14317 1575 2707 1578999 355737
454 read assemblies:
#ctgs min q1 q2 q3 max mean n50 sum 0cgv AMOScmp* 135 114 1012 4414 12554 110913 12255 36870 1654428 203524 CA 203 1002 2802 6431 12196 41845 8646 13047 1755208 245426 newbler** 48 131 883 9320 56233 210376 37056 112225 1778716 196515 SOAPdenovo 6531 45 103 179 306 1806 237 321 1553899 478469 velvet 21165 45 53 65 83 548 73 74 1561277 821841
Illumina & 454 read assemblies:
#ctgs min q1 q2 q3 max mean n50 sum 0cgv SOAPdenovo 5795 45 75 184 425 3983 317 588 1840810 243391 velvet 4229 45 135 269 507 3529 384 584 1626062 396716
Illumina & 454 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
Illumina & 454 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