Genome assembly (Week 3) Flashcards
Whole-genome shotgun (WGS) approach
Generating sequence reads directly from a whole-genome library
Using computational techniques (computer) to reassemble in one step
Whole-genome Shotgun
ADVANTAGES
- No mapping
- Time efficient
- Cost effective
Random – No redundant sequencing
Easy ‘Wet-lab”
Disadvantages
No mapping
Don’t know the location
Gaps difficult to resolve
Assembly very computationally intense
Difficult analysis
Whole-genome Shotgun sequencing
ADVANTAGES (3)
No mapping
- Time efficient
- Cost effective
Random – No redundant sequencing
Easy ‘Wet-lab”
Whole-genome shotgun sequencing
DISADVANTAGES (3)
No mapping
- Don’t know the location
- Gaps difficult to resolve
Assembly very computationally intense
Difficult analysis
Hierarchical shotgun approach
DEFINITION
Generating an overlapping set of intermediate-sized clones and keeping a map of that
BAC’s or YAC’s (Yeast Artificial chromosomes)
Hierarchical shotgun sequencing
ADVANTAGES & DISADVANTAGES
Advantages Easy assembly Know the location of reads Can easily re-sequence any area Less computationally intense
Disadvantages
Build library and physical map
Redundant sequencing
Hierarchical shotgun sequencing VS whole-genome shotgun sequencing
Hierarchical shotgun approach
- genome is broken into large fragments prior to sequencing
WGS approach
- the entire genome is broken into small fragments for sequencing