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Sequencing & Assembly

Methodology Overview

The Aedes aegypti genome was sequenced using the Whole Genome Shotgun methodology, whereby:

  1. DNA is shattered into small fragments (~4 kb or ~40 kb)
  2. Each fragment is inserted into a vector and cloned
  3. The two ends of the fragment are sequenced, creating paired reads
  4. The assembly process uses the paired reads to identify contiguous stretches of sequence (contigs)
  5. Contigs are ordered and linked together into larger supercontigs by using paired reads lying in different contigs

Assembly Data

Assembly 1, 8/1/2005

Sequencing Facts

  • Total length of assembly: 1.31 Gb
  • 7.63X (6.71X in Q20 bases)X sequencing coverage of the genome
  • 36206 contigs in 36206 scaffolds (supercontigs)
  • 1.31 Gb total length of combined contigs (1,310,090,344 bp)
  • Average base lies in a contig with length at least 82.6 Kb (contig N50)
  • Average base lies within a supercontig with length at least 1.5 Mb (supercontig N50)

Supercontig/Contig Numbering

  • 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 with 5.856 Mb, and supercontig 1.36206 is the smallest with 2.537 Kb.

    See the Assembly Structure for a list of all supercontigs with their lengths and contained contigs.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3... (in that order).

    See the Assembly Structure to explore the contigs of each supercontig or download a comma-separated file.

    There is no correspondence between contig or supercontigs numbers in different assemblies.