Sequencing & Assembly

Methodology Overview

The Saccharomyces cerevisiae RM11-1a genome was sequenced using the Whole Genome Shotgun methodology, whereby:

Saccharomyces cerevisiae RM11-1a 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
The assembly process uses the 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

Assembly 1, 9/10/2004

Total length of assembly: 11.737 Mb
10X sequencing coverage of the genome
115 contigs in 17 scaffolds (supercontigs)
11.675 Mb total length of combined contigs (11,675,031 bp)
Average base lies in a contig with length at least 263.3 Kb (contig N50)
Average base lies within a supercontig with length at least 794.9 Kb (supercontig N50)

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 1.481 Mb, and supercontig 1.17 is the smallest with 197.696 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...17 (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.

We end-sequenced the following types of libraries: Plasmid and Fosmid (F1_Saccharomyces_cerevisiae_rm11-1a)

Library Name	# Clone ends mapped to Assembly 1
Plasmid	141,355
Fosmid (F1_Saccharomyces_cerevisiae_rm11-1a)	31,289
total	172,644