Genome assembly2

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Contents

Lactobacillus genus

Circular view

NC 015214.png NC 015213.png NC 015218.png

copy # and position of rRNA operon

Terminus

rRNA operon of Other species

NamerRNA operonTotal Lentransposase
Lactobacillus_acidophilus_NCFM42M40
Lactobacillus_brevis_ATCC_36752.2M
Lactobacillus_casei53M
Lactobacillus_casei_ATCC_33452.9M
Lactobacillus_casei_Zhang_uid5067352.8M
Lactobacillus_crispatus_ST1_uid4835942M
Lactobacillus_delbrueckii_bulgaricus91.8M
Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-36591.8M
Lactobacillus_fermentum_IFO_395652.1M
Lactobacillus_gasseri_ATCC_3332361.9M
Lactobacillus_helveticus_DPC_457142.1M 260
Lactobacillus_johnsonii_FI978541.8M
Lactobacillus_johnsonii_NCC_5336 2M
Lactobacillus_plantarum53.3M
Lactobacillus_plantarum_JDM153.2M
Lactobacillus_reuteri_DSM_2001662M
Lactobacillus_reuteri_F275_Kitasato62M
Lactobacillus_rhamnosus_GG53M
Lactobacillus_rhamnosus_Lc_70553M
Lactobacillus_sakei_23K71.9M
Lactobacillus_salivarius_UCC11871.8M

Read

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)

Assembly flow


Assembly Result

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 *very bad, reject
Newbler(454 only), gapResolution Scaffolds 15 2058137 Running PCR
Newbler(454 only), gapResolution Contigs 21 2053877 Running PCR
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


Links

Scripts

Etc

  1. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
    1. SR assembly Tutorial
  2. High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies
  3. De novo bacterial genome sequencing: Millions of very short reads ...
  4. Short read fragment assembly of bacterial genomes...
  5. De novo fragment assembly with short mate-paired reads: Does the read length matter? (PDF)
  1. sequence quality in solexa format
  1. A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000, MPMI(2008) (PDF)
  2. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics (2008)
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