Currently the 454 pyrosequencing technology is considered as a rapid and economical method to generate high-quantity sequence data.
Some challenges are computational and result from the huge quantity of sequence data.
Independently of assembly problems, functional annotation is a difficult problem, compounded by the sheer quantity of sequence data.
Despite research into the behavior and classical and population genetics of this organism, the quantity of sequence data available is limited.
The goal of the super-read algorithm is to reduce the quantity of sequence data presented to the overlap-based assembler.
The advent of commercial second generation sequencing machines has lead to new strategies for developing EST-SSR markers, necessitating the development of bioinformatic framework that can keep pace with the increasing quality and quantity of sequence data produced.
Next-generation sequencing offers a lower-cost option to generate a large quantity of sequence data for nonmodel species without the use of cloning, which is restricted in New Zealand for native species such as F. excorticata.
Despite the cost effective advantages a pooled sample approach delivers, given a fixed quantity of sequence data, a compromise on the fold-coverage per pooled sample/group and thereby sensitivity is unavoidable.
With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data.
We explicitly model the effects of variation in gene tree topology in our work, and explore both the overall gains in phylogenetic resolution, and the ability to recover particular problematic nodes with high support values with a substantial increase in the quantity of sequence data.
The flexibility to roll-your-own workflow enables the user to tackle both prokaryotic and eukaryotic assembly projects, tailoring the amount of work to be done based on the availability of computing resources, quantity of sequence data and complexity of the genome.
