Sequencing & Assembly
Whole Genome Shotgun Overview
These genomes were sequenced with 454 and/or Sanger Whole Genome Shotgun methodology:
- DNA is shattered into small fragments (~4 kb or ~40 kb)
- Each fragment is inserted into a vector and cloned
- The two ends of the fragment are sequenced, creating paired reads
- DNA is shattered into small fragments (~0.6kb or~3kb)
- 0.6kb fragments are tailed with 454 sequencing adapters
- 3kb fragments are circularized on a biotinylated linker, circles are sheared, fragments containing biotinylated linker are retrieved and tailed with 454 sequencing adapters.
- Adapterized fragments are sequenced from one end, creating fragment or paired reads.
Arachne or Newbler (454 Life Sciences) Assembly
- The assembly process uses fragment and paired reads to identify contiguous stretches of sequence (contigs)
- Contigs are ordered and linked together into larger supercontigs by using paired reads lying in different contigs
For more info on the arachne assembler see our CRD page.
- Supercontig and contig numbers are preceded by the version of the assembly. For example:
- Contig 1.25 - refers to contig number 25 within assembly 1.
- Supercontig 1.2 - refers to supercontig number 2 within assembly 1.
- Supercontigs are numbered in order of decreasing length. For example, supercontig 1.1 is the largest, and supercontig 1.2 is the next largest.
- Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3... (in that order).
There is no correspondence between contig or supercontigs numbers in different assemblies.