Figure 1. Strategy of international human genome sequencing consortium is based on selecting a minimal set of overlapping bacterial artificial chromosome (BAC) clones to sequence, from libraries covering the genome many times. Each selected clone then undergoes shotgun sequencing to a certain base coverage and is then ‘finished’ to close the remaining gaps and resolve problems in a semi-manual fashion. A shotgun coverage of 4X means that on average each base in the clonexf will occur in four different reads.

Figure 2. Finger print contigs (FPCs) are positioned and orientated on human chromosomes via Généthon markers and radiation hybrid (RH) map. Each FPC is an assembly of BAC clones based on similarities between their restriction digest fingerprints.

Figure 3. (a) The raw human genome sequence consists of a mixture of sequences of finished (one continuous sequence) and unfinished (between 2 and 20 fragments) clones, available from the public sequences databases. The initial order of the clones is taken from FPCs. Within an unfinished clone, some fragments are locally ordered on the basis of paired reads, but the rest are unordered. As an unfinished clone is worked on to take it to finished status, it is resubmitted to the public databases, each time keeping its original accession number, but incrementing its version number. (b) The current set of sequences in public databases is defined as a freeze, and identified by their accession and version numbers, so subsequent analysis all works with the same set of sequences. Sequence homology searches between fragments in this set find overlaps that are consistent, or nearly consistent, with the original clone order (H). (c) A golden path is defined as the ordered set of fragments from the freeze which uniquely defines a nonredundant genome sequence, with strings of N's inserted to mark known gaps between fragments (G). Gaps can occur between ordered or unordered fragments within clones (G1) or between clones (G2) where no significant sequence similarity was found between their fragments.