This method will be completed using a 10x redundancy

•
This method will be completed using a 10x redundancy to eliminate
errors and reduce the possibility of having misses any targeted regions.
•
The Celera Assembler is one of the core competencies and makes this
Herculean task possible.
•
The first pass through the data the shotgunned fragments are compared
against each other and equivalent sequences greater than 40 base pairs
long identified.
•
These 40 base pairs matches are statistically impossible to occur by
chance. These matches are then determined to be true or repeat
induced. True matches are overlapping sections and are the desired
fragments; repeat-induced fragments occur in multiple locations of the
genome and do not belong together.

Whole Genome Shotgun
Sequencing
•
The assembler then searches for overlapping fragments that have a
common sequence and are not contested elsewhere in the dataset.
•
The uncontested data is assembled into unitigs containing
approximately 30 fragments.
•
These assembled unitigs are 99 % accurate and repeats are filtered out
using the Discriminator algorithm.
•
Unitigs passing this filter are identified and renamed U-untigs that are
ready for ordering.
•
The scaffolding stage starts and the order found by looking at the mate
pairs and organizing these into contigs. By constantly looking at these
contigs and looking at the orientation the scaffold become complete
except for some sequencing gaps.
•
This strategy is repeated until the gaps are filled using the
Discriminator algorithm and a method using sequence “rocks” and
“pebbles”.

Whole Genome Shotgun
Sequencing
•
As HGP has been making public the
incremental sequence the shotgun approach
utilized this data to help eliminate errors
and speed the scaffolding process.

Sequence Gaps
Brown. Genomes 2

Advances
•
The following advances in robotics and automation
reduced the labor by 80% while combining the
microbiological advances:
–
Development of Perkin-Elmer (ABI PRISM 3700) gene sequence.
–
1000 sample per day
–
15 minutes instead of 8 hours for first automated sequencers
–
A parallel system of 300 sequencers ($300,000 each)
–
Use of supercomputers to assemble fragments
•
Development of process support instrumentation to
process 100 K template preps and 200 K sequence
reactions per day.
•
24 hour per day unattended operation of sequencers

Map of Chromosome 16

Advances
•
In addition to the above advances the field of
computational biology (bioinformatics) became
increasingly important as the software and
processors required to assemble a puzzle of this
size still needed to be developed.