Scaffolding (bioinformatics)

The success of this strategy prompted The Institute for Genomic Research to develop the scaffolding program Grouper for their other sequencing projects.

Bambus was created in 2003 and was a rewrite of the original grouper software, but afforded researchers the ability to adjust scaffolding parameters.

SSPACE also uses a greedy algorithm that begins building its first scaffold with the longest contig provided by the sequence data.

[8] Utturkar et al. investigated the utility of several different assembly software packages in combination with hybrid sequence data.

These new platforms are able to generate large quantities of data in short periods of time, but until methods were developed for de novo assembly of large genomes from short read sequences, Sanger sequencing remained the standard method of creating a reference genome.

The increased difficulty of contig and scaffold assembly associated with the new technologies has created a demand for powerful new computer programs and algorithms capable of making sense of the data.

The release of the SMRT platform, from Pacific Biosciences, marked the beginning of single molecule sequencing and long read tech.

It has been shown that 80-100X coverage with SMRT technology, which generates average read with lengths of 5456bp, is usually sufficient to create a finished de novo assembly for prokaryotic organisms.