Genome2

From CSBLwiki

Contents 1 Basic Statistics 1.1 de novo assembly by velvet 1.2 Newbler 1.3 ABySS 1.4 Terminus 1.5 copy # and position of rRNA operon 1.6 comparative 1.6.1 rRNA operon of Other species 2 Read 3 Softwares 4 Links 4.1 Scripts 4.2 Etc

Basic Statistics

de novo assembly by velvet

1. contig fragments: 14,702
2. ave. length: 182 bp, Min=31, Max=51,398
3. Sum: 2,674,691 nt. (2.6 Mbp)
4. 80%: < 200 nt.

Newbler

ABySS

Terminus

• scf13 : oriC, 155nt, 56722..56876 nt
• scf10_4

copy # and position of rRNA operon

• copy # : 4
• position
  • 2h,3h, 5t, 7h, 9h, 11h, 13h

comparative

1. assembling by 15 known Lactobacillus genomes

rRNA operon of Other species

Lactobacillus_acidophilus_NCFM	4	2M
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
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
  • error probabilities : [[1]]
  • Almost reads are about 13 score.
  • It means the base call accuracy is about 95%.
  • Using fastq_quality_filter (FASTX_Toolkit), good reads are chosen. The parameters are... Qualitiy cut-off:13 ,Minimum percentage of bases that must have [-q] quality: 97 (35bp of 36bp)
    • The passed reads are 4508430. It is about 86% or total reads.
• Roche 454 reads 1: paired-end, 270784(158188) reads
• Roche 454 reads 2: paired-end, 364291(235924) reads

Softwares

• Related softwares & their links
• comparative

1. Maq (Mapping and Assembly with Qualities)
   1. Manual
2. AMOScmp Comparative assembly package
3. SOAP Short Oligonucleotide Analysis Package

• de novo assembly

1. de Bruijn graphs
   1. velvet
   2. abyss 1.0.5
2. suffix tree-based approach
   1. QSRA
   2. SSAKE
   3. VCAKE
3. overlap-layout-consensus
   1. edena
4. ??
   1. SHARCGS
   2. ALLPATHS

• ab initio assembly

1. PCAP & CAP3 assembler
2. Phrap
3. ARACHNE
4. EULER
5. amos-minimus2
6. Newbler
7. wgs

• alignment

1. exonerate a generic tool for sequence alignment
2. Manatee Web-based annotation system
3. local blast NCBI BLAST

Links

Scripts

• Various Perl Scripts

Etc

• NCBI Genomes
• Lactobacillus delbrueckii bulgaricus by Genoscope
• Tech Summary: Illumina's Solexa Sequencing Technology
• Case stuides:

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)

• Solexa format & Fastq format

1. sequence quality in solexa format

• Benchmark papers

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)