Genome Annotation and Assembly

The entire genome of an organism cannot be sequenced in continuous sequences - even the newest generation of sequencing technologies produce fragmented data from thousands of short DNA fragments ranging from 50-1000bp in length.

These short DNA sequences - called reads - need to be assembled to reconstruct the complete sequence of a genome in a process called genome assembly.

There are four main steps in any next-generation genome assembly - raw data analysis, contig assembly, scaffolding, and finally, gap closing.

The first step is to analyze the raw data acquired for quality - and then eliminate any contamination, biased data, or poor quality reads with a large number of unknown nucleotides.

Next, the clean reads are trimmed to remove the adapter sequences from their ends. Any bases at the fragment ends that do not pass the quality threshold are also trimmed.

Then, a well-suited assembly tool is used to assemble the reads into contiguous sequences - called contigs - based on the overlapping DNA segments.

Comparative genome assembly can be used when a reference genome of a closely related organism is available to direct the reconstruction of the new genome. Here, the reads are ali