The biggest challenges for us as scientists lie in deciding which company would be the most suitable for synthesizing specific sequences (such as large plasmids from scratch, or exotic nucleotide containing sequences), and as each company has dedicated interfaces for formatting the provided data, not every biologist finds is easy to re-do the whole process.
Scientists usually go through comparisons of each company's capabilities in terms of turnaround time, sequence-fidelity, chemical versus enzymatic synthesis and costs, which becomes a laborious process especially for early-stage professionals.
From personal experience, most of the time we'd need to reach out to various company representatives individually to receive their personalized feedback and recommendation, as the sites did not allow such automation. Depending on service providers, this can lead to a very time consuming workflow, especially if the experiments need to be carried out rapidly.
Our Project goal is to automate the process in one way or another.