Sequencing & Assembly

Methodology Overview

The Batrachochytrium dendrobatidis genome was sequenced using the Whole Genome Shotgun methodology, whereby:

  1. Batrachochytrium dendrobatidis 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, September 7, 2006

Sequencing Facts

  • Total length of assembly: 23.699 Mb
  • 7.40 (6.44 q>20)X sequencing coverage of the genome
  • 348 contigs in 69 scaffolds (supercontigs)
  • 23.404 Mb total length of combined contigs (23,403,618 bp)
  • Average base lies in a contig with length at least 221.037 Kb (contig N50)
  • Average base lies within a supercontig with length at least 1.706 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 4.439 Mb, and supercontig 1.69 is the smallest with 2.608 Kb.
  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3...69 (in that order).

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