Genome assembly2
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*Roche 454 reads 1: paired-end, 270784(158188) reads | *Roche 454 reads 1: paired-end, 270784(158188) reads | ||
*Roche 454 reads 2: paired-end, 364291(235924) reads | *Roche 454 reads 2: paired-end, 364291(235924) reads | ||
+ | |||
+ | ==Assembly flow== | ||
+ | *illumina -> ABySS: 4336 contigs, total 4M; very bad -> fake reads | ||
+ | *fake reads(ABySS illumina) + 454reads -> Newbler : 443 scaffolds; very bad => reject | ||
+ | |||
+ | |||
+ | *only 454 -> Newbler,gapResolution -> 15scf, 21ctg -> '''Running PCR NOW''' | ||
+ | *only 454 -> CABOG -> compare(mapping) to Newbler (by nucmer & mummerplot) -> '''some disagree in scaffolds between 2 softwares''' | ||
+ | |||
+ | |||
+ | |||
==Assembly Result== | ==Assembly Result== | ||
{| class="wikitable" style="text-align:center" border="1" | {| class="wikitable" style="text-align:center" border="1" | ||
|+ | |+ | ||
|- | |- | ||
- | | | + | |Flatform || Read Type || Total Reads || Number of Reads Used || Number of Bases Used || Percent Reads Assembled || Percent Bases Assembled |
|- | |- | ||
- | | | + | |Solexa Illumina || SE || 5359073 || - || - || - || - |
- | | | + | |
|- | |- | ||
+ | | Fake Reads(FR) (Solexa/Illumina)|| SE || 8390 || 11964248|| 8243 || 98.25 || 95.15 | ||
+ | |- | ||
+ | | FR (CABOG) || SE || 7020 || 10529913 || 7017 || 99.96 || 99.93 | ||
+ | |- | ||
+ | | Roche 454 || PE || 158188 (270784) || || || || || | ||
+ | |- | ||
+ | | Roche 454 || PE || 235924 (364291) || || || || || | ||
+ | |} | ||
+ | {| class="wikitable" style="text-align:center" border="1" | ||
+ | |+ | ||
+ | |- | ||
+ | |Assembler || Contig Type || Number of Contigs || Total bases || | ||
+ | |- | ||
+ | |velvet || contigs || 14702 || 2674691 || | ||
+ | |- | ||
+ | |ABySS || Large Contig (>500bp) || 4336 || 4121677 || *very bad | ||
+ | |- | ||
+ | |Newbler(FR(Sol/Ill) + 454 || Scaffolds || 443 || 4585959 || | ||
+ | |- | ||
+ | |Newbler(454 only), gapResolution || Scaffolds || 15 || 2058137 || | ||
+ | |- | ||
+ | |Newbler(454 only), gapResolution || Contigs || 21 || 2053877 || | ||
+ | |- | ||
+ | |CABOG(454 only) || Scaffolds (>500bp)|| 13 || 2120461 || | ||
+ | |- | ||
+ | |CABOG(454 only) || Contigs (>500bp) || 26 || 2119042 || | ||
+ | |- | ||
+ | |Newbler(FR(CABOG) +454) || Scaffolds || 7 || 2051269 || | ||
+ | |- | ||
+ | |Newbler(FR(CABOG) +454) || Scaffolds || 59 || 2012620 || | ||
|} | |} |
Revision as of 14:28, 19 October 2010
Contents |
Lactobacillus genus
copy # and position of rRNA operon
- copy # : 4
- position
- 2h,3h, 5t, 7h, 9h, 11h, 13h
Terminus
- scf13 : oriC, 155nt, 56722..56876 nt
- scf10_4
rRNA operon of Other species
Name | rRNA operon | Total Len | transposase |
Lactobacillus_acidophilus_NCFM | 4 | 2M | 40 |
Lactobacillus_brevis_ATCC_367 | 5 | 2.2M | |
Lactobacillus_casei | 5 | 3M | |
Lactobacillus_casei_ATCC_334 | 5 | 2.9M | |
Lactobacillus_casei_Zhang_uid50673 | 5 | 2.8M | |
Lactobacillus_crispatus_ST1_uid48359 | 4 | 2M | |
Lactobacillus_delbrueckii_bulgaricus | 9 | 1.8M | |
Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365 | 9 | 1.8M | |
Lactobacillus_fermentum_IFO_3956 | 5 | 2.1M | |
Lactobacillus_gasseri_ATCC_33323 | 6 | 1.9M | |
Lactobacillus_helveticus_DPC_4571 | 4 | 2.1M | 260 |
Lactobacillus_johnsonii_FI9785 | 4 | 1.8M | |
Lactobacillus_johnsonii_NCC_533 | 6 | 2M | |
Lactobacillus_plantarum | 5 | 3.3M | |
Lactobacillus_plantarum_JDM1 | 5 | 3.2M | |
Lactobacillus_reuteri_DSM_20016 | 6 | 2M | |
Lactobacillus_reuteri_F275_Kitasato | 6 | 2M | |
Lactobacillus_rhamnosus_GG | 5 | 3M | |
Lactobacillus_rhamnosus_Lc_705 | 5 | 3M | |
Lactobacillus_sakei_23K | 7 | 1.9M | |
Lactobacillus_salivarius_UCC118 | 7 | 1.8M |
Read
- Solexa Illumina reads : single-end, 36bp, 5359073 reads
- Roche 454 reads 1: paired-end, 270784(158188) reads
- Roche 454 reads 2: paired-end, 364291(235924) reads
Assembly flow
- illumina -> ABySS: 4336 contigs, total 4M; very bad -> fake reads
- fake reads(ABySS illumina) + 454reads -> Newbler : 443 scaffolds; very bad => reject
- only 454 -> Newbler,gapResolution -> 15scf, 21ctg -> Running PCR NOW
- only 454 -> CABOG -> compare(mapping) to Newbler (by nucmer & mummerplot) -> some disagree in scaffolds between 2 softwares
Assembly Result
Flatform | Read Type | Total Reads | Number of Reads Used | Number of Bases Used | Percent Reads Assembled | Percent Bases Assembled | |
Solexa Illumina | SE | 5359073 | - | - | - | - | |
Fake Reads(FR) (Solexa/Illumina) | SE | 8390 | 11964248 | 8243 | 98.25 | 95.15 | |
FR (CABOG) | SE | 7020 | 10529913 | 7017 | 99.96 | 99.93 | |
Roche 454 | PE | 158188 (270784) | |||||
Roche 454 | PE | 235924 (364291) |
Assembler | Contig Type | Number of Contigs | Total bases | |
velvet | contigs | 14702 | 2674691 | |
ABySS | Large Contig (>500bp) | 4336 | 4121677 | *very bad |
Newbler(FR(Sol/Ill) + 454 | Scaffolds | 443 | 4585959 | |
Newbler(454 only), gapResolution | Scaffolds | 15 | 2058137 | |
Newbler(454 only), gapResolution | Contigs | 21 | 2053877 | |
CABOG(454 only) | Scaffolds (>500bp) | 13 | 2120461 | |
CABOG(454 only) | Contigs (>500bp) | 26 | 2119042 | |
Newbler(FR(CABOG) +454) | Scaffolds | 7 | 2051269 | |
Newbler(FR(CABOG) +454) | Scaffolds | 59 | 2012620 |