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Sequencing & Assembly

Methodology Overview

The Culex pipiens genome was sequenced using the Whole Genome Shotgun methodology, whereby:

  1. Culex pipiens 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 3, December 15, 2006

Sequencing Facts

  • Total length of assembly: 539.959 Mb
  • 6.14 (5.30 q>20)X sequencing coverage of the genome
  • 48671 contigs in 3171 scaffolds (supercontigs)
  • 539.959 Mb total length of combined contigs (539,959,374 bp)
  • Average base lies in a contig with length at least 28.546 Kb (contig N50)
  • Average base lies within a supercontig with length at least 475.607 Kb (supercontig N50)

Supercontig/Contig Numbering

  • Supercontig and contig numbers are preceded by the version of the assembly. For example:
    • Contig 3.25 - refers to contig number 25 within assembly 3.
    • Supercontig 3.2 - refers to supercontig number 2 within assembly 3.

  • Supercontigs are numbered in order of decreasing length. For example, supercontig 3.1 is the largest with 3.806 Mb, and supercontig 3.3171 is the smallest with 1.197 Kb.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 3.1 contains contigs 1,2,3...3171 (in that order).

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