Sequence Assembly - Genome Assemblers

Genome Assemblers

The first sequence assemblers began to appear in the late 1980s and early 1990s as variants of simpler sequence alignment programs to piece together vast quantities of fragments generated by automated sequencing instruments called DNA sequencers. As the sequenced organisms grew in size and complexity (from small viruses over plasmids to bacteria and finally eukaryotes), the assembly programs used in these genome projects needed to increasingly employ more and more sophisticated strategies to handle:

• terabytes of sequencing data which need processing on computing clusters;
• identical and nearly identical sequences (known as repeats) which can, in the worst case, increase the time and space complexity of algorithms exponentially;
• and errors in the fragments from the sequencing instruments, which can confound assembly.

Faced with the challenge of assembling the first larger eukaryotic genomes, the fruit fly Drosophila melanogaster, in 2000 and the human genome just a year later, scientists developed assemblers like Celera Assembler and Arachne able to handle genomes of 100-300 million base pairs. Subsequent to these efforts, several other groups, mostly at the major genome sequencing centers, built large-scale assemblers, and an open source effort known as AMOS was launched to bring together all the innovations in genome assembly technology under the open source framework.