Genome2
From CSBLwiki
Contents |
Basic Statistics
de novo assembly by velvet
- contig fragments: 14,702
- ave. length: 182 bp, Min=31, Max=51,398
- Sum: 2,674,691 nt. (2.6 Mbp)
- 80%: < 200 nt.
strategy
- assembling by 15 known Lactobacillus genomes
Softwares
- Related softwares & their links
- comparative
- Maq (Mapping and Assembly with Qualities)
- AMOScmp Comparative assembly package
- SOAP Short Oligonucleotide Analysis Package
- de novo assembly
- de Bruijn graphs
- velvet
- abyss 1.0.5
- suffix tree-based approach
- QSRA
- SSAKE
- VCAKE
- overlap-layout-consensus
- edena
- ??
- SHARCGS
- ALLPATHS
- ab initio assembly
- PCAP & CAP3 assembler
- Phrap
- ARACHNE
- EULER
- amos-minimus2
- Newbler
- wgs
- alignment
- exonerate a generic tool for sequence alignment
- Manatee Web-based annotation system
- local blast NCBI BLAST
Links
Scripts
Etc
- NCBI Genomes
- Lactobacillus delbrueckii bulgaricus by Genoscope
- Tech Summary: Illumina's Solexa Sequencing Technology
- Case stuides:
- Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
- High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies
- De novo bacterial genome sequencing: Millions of very short reads ...
- Short read fragment assembly of bacterial genomes...
- De novo fragment assembly with short mate-paired reads: Does the read length matter? (PDF)
- Solexa format & Fastq format
- Benchmark papers
- 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)
- High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi, Nature Genetics (2008)